From 26e0796f4c10f49ba21edfe7cc8c087df0aebabb Mon Sep 17 00:00:00 2001 From: Andrew Butler Date: Thu, 5 Dec 2019 09:51:56 -0500 Subject: [PATCH 1/8] update docs for patch release - new roxygen2 version --- DESCRIPTION | 6 +- man/AddMetaData.Rd | 1 - man/AddModuleScore.Rd | 16 +++- man/AverageExpression.Rd | 15 +++- man/BuildClusterTree.Rd | 14 +++- man/CalculateBarcodeInflections.Rd | 10 ++- man/CellCycleScoring.Rd | 3 +- man/CellScatter.Rd | 12 ++- man/CollapseEmbeddingOutliers.Rd | 10 ++- man/CollapseSpeciesExpressionMatrix.Rd | 8 +- man/ColorDimSplit.Rd | 53 +++++++------ man/CreateDimReducObject.Rd | 15 +++- man/CreateGeneActivityMatrix.Rd | 12 ++- man/CreateSeuratObject.Rd | 13 ++- man/DietSeurat.Rd | 12 ++- man/DimHeatmap.Rd | 21 ++++- man/DimPlot.Rd | 28 +++++-- man/DoHeatmap.Rd | 27 +++++-- man/DotPlot.Rd | 19 ++++- man/ExportToCellbrowser.Rd | 19 +++-- man/FeaturePlot.Rd | 34 ++++++-- man/FeatureScatter.Rd | 16 +++- man/FindAllMarkers.Rd | 27 +++++-- man/FindClusters.Rd | 51 +++++++++--- man/FindConservedMarkers.Rd | 14 +++- man/FindIntegrationAnchors.Rd | 24 ++++-- man/FindMarkers.Rd | 63 +++++++++++---- man/FindNeighbors.Rd | 78 +++++++++++++----- man/FindTransferAnchors.Rd | 26 ++++-- man/FindVariableFeatures.Rd | 63 ++++++++++----- man/GetResidual.Rd | 11 ++- man/HTODemux.Rd | 14 +++- man/HTOHeatmap.Rd | 13 ++- man/HVFInfo.Rd | 3 +- man/Idents.Rd | 15 ++-- man/IntegrateData.Rd | 21 +++-- man/JackStraw.Rd | 13 ++- man/JackStrawPlot.Rd | 3 +- man/LabelClusters.Rd | 11 ++- man/LabelPoints.Rd | 11 ++- man/Loadings.Rd | 3 +- man/LocalStruct.Rd | 13 ++- man/MULTIseqDemux.Rd | 12 ++- man/MetaFeature.Rd | 10 ++- man/MixingMetric.Rd | 12 ++- man/NormalizeData.Rd | 35 ++++++--- man/OldWhichCells.Rd | 30 +++++-- man/PCASigGenes.Rd | 9 ++- man/PercentageFeatureSet.Rd | 9 ++- man/PolyDimPlot.Rd | 9 ++- man/PolyFeaturePlot.Rd | 14 +++- man/PrepSCTIntegration.Rd | 9 ++- man/ProjectDim.Rd | 13 ++- man/RenameCells.Rd | 9 ++- man/RidgePlot.Rd | 19 ++++- man/RunALRA.Rd | 36 +++++++-- man/RunCCA.Rd | 30 +++++-- man/RunICA.Rd | 60 ++++++++++---- man/RunLSI.Rd | 39 +++++++-- man/RunPCA.Rd | 59 ++++++++++---- man/RunTSNE.Rd | 65 +++++++++++---- man/RunUMAP.Rd | 105 ++++++++++++++++++------- man/SCTransform.Rd | 26 ++++-- man/ScaleData.Rd | 67 ++++++++++++---- man/ScoreJackStraw.Rd | 20 +++-- man/SelectIntegrationFeatures.Rd | 10 ++- man/SetAssayData.Rd | 3 +- man/SeuratTheme.Rd | 10 ++- man/SubsetData.Rd | 30 +++++-- man/TopFeatures.Rd | 10 ++- man/TransferData.Rd | 16 +++- man/UpdateSymbolList.Rd | 18 ++++- man/VariableFeaturePlot.Rd | 10 ++- man/VariableFeatures.Rd | 3 +- man/VizDimLoadings.Rd | 14 +++- man/VlnPlot.Rd | 23 +++++- man/WhichCells.Rd | 17 ++-- man/as.Seurat.Rd | 27 +++++-- man/as.loom.Rd | 26 +++--- man/as.sparse.Rd | 13 ++- man/h5ad.Rd | 17 ++-- man/merge.Seurat.Rd | 13 ++- man/print.DimReduc.Rd | 3 +- man/subset.Seurat.Rd | 3 +- 84 files changed, 1343 insertions(+), 461 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 929917ea0..c132dab29 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Seurat -Version: 3.1.1.9023 -Date: 2019-12-04 +Version: 3.1.2 +Date: 2019-12-08 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , and Butler A and Satija R (2017) for more details. Authors@R: c( @@ -81,7 +81,7 @@ Collate: 'tree.R' 'utilities.R' 'zzz.R' -RoxygenNote: 6.1.1 +RoxygenNote: 7.0.2 Encoding: UTF-8 Suggests: loomR, diff --git a/man/AddMetaData.Rd b/man/AddMetaData.Rd index 58f337942..4cd1823b8 100644 --- a/man/AddMetaData.Rd +++ b/man/AddMetaData.Rd @@ -1,6 +1,5 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/generics.R, R/objects.R -\docType{methods} \name{AddMetaData} \alias{AddMetaData} \alias{SeuratAccess} diff --git a/man/AddModuleScore.Rd b/man/AddModuleScore.Rd index 05324f657..0ca38567b 100644 --- a/man/AddModuleScore.Rd +++ b/man/AddModuleScore.Rd @@ -4,9 +4,19 @@ \alias{AddModuleScore} \title{Calculate module scores for feature expression programs in single cells} \usage{ -AddModuleScore(object, features, pool = NULL, nbin = 24, ctrl = 100, - k = FALSE, assay = NULL, name = "Cluster", seed = 1, - search = FALSE, ...) +AddModuleScore( + object, + features, + pool = NULL, + nbin = 24, + ctrl = 100, + k = FALSE, + assay = NULL, + name = "Cluster", + seed = 1, + search = FALSE, + ... +) } \arguments{ \item{object}{Seurat object} diff --git a/man/AverageExpression.Rd b/man/AverageExpression.Rd index aa279a5bc..668ddb269 100644 --- a/man/AverageExpression.Rd +++ b/man/AverageExpression.Rd @@ -4,9 +4,18 @@ \alias{AverageExpression} \title{Averaged feature expression by identity class} \usage{ -AverageExpression(object, assays = NULL, features = NULL, - return.seurat = FALSE, add.ident = NULL, slot = "data", - use.scale = FALSE, use.counts = FALSE, verbose = TRUE, ...) +AverageExpression( + object, + assays = NULL, + features = NULL, + return.seurat = FALSE, + add.ident = NULL, + slot = "data", + use.scale = FALSE, + use.counts = FALSE, + verbose = TRUE, + ... +) } \arguments{ \item{object}{Seurat object} diff --git a/man/BuildClusterTree.Rd b/man/BuildClusterTree.Rd index 0ebde224b..e43fa9ed6 100644 --- a/man/BuildClusterTree.Rd +++ b/man/BuildClusterTree.Rd @@ -4,9 +4,17 @@ \alias{BuildClusterTree} \title{Phylogenetic Analysis of Identity Classes} \usage{ -BuildClusterTree(object, assay = NULL, features = NULL, dims = NULL, - graph = NULL, slot = "data", reorder = FALSE, - reorder.numeric = FALSE, verbose = TRUE) +BuildClusterTree( + object, + assay = NULL, + features = NULL, + dims = NULL, + graph = NULL, + slot = "data", + reorder = FALSE, + reorder.numeric = FALSE, + verbose = TRUE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/CalculateBarcodeInflections.Rd b/man/CalculateBarcodeInflections.Rd index d386ad7da..878cbdc38 100644 --- a/man/CalculateBarcodeInflections.Rd +++ b/man/CalculateBarcodeInflections.Rd @@ -4,9 +4,13 @@ \alias{CalculateBarcodeInflections} \title{Calculate the Barcode Distribution Inflection} \usage{ -CalculateBarcodeInflections(object, barcode.column = "nCount_RNA", - group.column = "orig.ident", threshold.low = NULL, - threshold.high = NULL) +CalculateBarcodeInflections( + object, + barcode.column = "nCount_RNA", + group.column = "orig.ident", + threshold.low = NULL, + threshold.high = NULL +) } \arguments{ \item{object}{Seurat object} diff --git a/man/CellCycleScoring.Rd b/man/CellCycleScoring.Rd index 9bdf6cdeb..4cbef5feb 100644 --- a/man/CellCycleScoring.Rd +++ b/man/CellCycleScoring.Rd @@ -4,8 +4,7 @@ \alias{CellCycleScoring} \title{Score cell cycle phases} \usage{ -CellCycleScoring(object, s.features, g2m.features, set.ident = FALSE, - ...) +CellCycleScoring(object, s.features, g2m.features, set.ident = FALSE, ...) } \arguments{ \item{object}{A Seurat object} diff --git a/man/CellScatter.Rd b/man/CellScatter.Rd index dfa6ff14d..de0383621 100644 --- a/man/CellScatter.Rd +++ b/man/CellScatter.Rd @@ -5,8 +5,16 @@ \alias{CellPlot} \title{Cell-cell scatter plot} \usage{ -CellScatter(object, cell1, cell2, features = NULL, highlight = NULL, - cols = NULL, pt.size = 1, smooth = FALSE) +CellScatter( + object, + cell1, + cell2, + features = NULL, + highlight = NULL, + cols = NULL, + pt.size = 1, + smooth = FALSE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/CollapseEmbeddingOutliers.Rd b/man/CollapseEmbeddingOutliers.Rd index e80e74355..68610f432 100644 --- a/man/CollapseEmbeddingOutliers.Rd +++ b/man/CollapseEmbeddingOutliers.Rd @@ -4,8 +4,14 @@ \alias{CollapseEmbeddingOutliers} \title{Move outliers towards center on dimension reduction plot} \usage{ -CollapseEmbeddingOutliers(object, reduction = "umap", dims = 1:2, - group.by = "ident", outlier.sd = 2, reduction.key = "UMAP_") +CollapseEmbeddingOutliers( + object, + reduction = "umap", + dims = 1:2, + group.by = "ident", + outlier.sd = 2, + reduction.key = "UMAP_" +) } \arguments{ \item{object}{Seurat object} diff --git a/man/CollapseSpeciesExpressionMatrix.Rd b/man/CollapseSpeciesExpressionMatrix.Rd index 013671e87..53c2b8811 100644 --- a/man/CollapseSpeciesExpressionMatrix.Rd +++ b/man/CollapseSpeciesExpressionMatrix.Rd @@ -4,8 +4,12 @@ \alias{CollapseSpeciesExpressionMatrix} \title{Slim down a multi-species expression matrix, when only one species is primarily of interenst.} \usage{ -CollapseSpeciesExpressionMatrix(object, prefix = "HUMAN_", - controls = "MOUSE_", ncontrols = 100) +CollapseSpeciesExpressionMatrix( + object, + prefix = "HUMAN_", + controls = "MOUSE_", + ncontrols = 100 +) } \arguments{ \item{object}{A UMI count matrix. Should contain rownames that start with diff --git a/man/ColorDimSplit.Rd b/man/ColorDimSplit.Rd index c69611570..a2a85b4bc 100644 --- a/man/ColorDimSplit.Rd +++ b/man/ColorDimSplit.Rd @@ -4,8 +4,14 @@ \alias{ColorDimSplit} \title{Color dimensional reduction plot by tree split} \usage{ -ColorDimSplit(object, node, left.color = "red", right.color = "blue", - other.color = "grey50", ...) +ColorDimSplit( + object, + node, + left.color = "red", + right.color = "blue", + other.color = "grey50", + ... +) } \arguments{ \item{object}{Seurat object} @@ -18,41 +24,42 @@ ColorDimSplit(object, node, left.color = "red", right.color = "blue", \item{other.color}{Color for all other cells} -\item{...}{Arguments passed on to \code{DimPlot} -\describe{ - \item{dims}{Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions} - \item{cells}{Vector of cells to plot (default is all cells)} - \item{cols}{Vector of colors, each color corresponds to an identity class. This may also be a single character +\item{...}{ + Arguments passed on to \code{\link[=DimPlot]{DimPlot}} + \describe{ + \item{\code{dims}}{Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions} + \item{\code{cells}}{Vector of cells to plot (default is all cells)} + \item{\code{cols}}{Vector of colors, each color corresponds to an identity class. This may also be a single character or numeric value corresponding to a palette as specified by \code{\link[RColorBrewer]{brewer.pal.info}}. By default, ggplot2 assigns colors} - \item{pt.size}{Adjust point size for plotting} - \item{reduction}{Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca} - \item{group.by}{Name of one or more metadata columns to group (color) cells by + \item{\code{pt.size}}{Adjust point size for plotting} + \item{\code{reduction}}{Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca} + \item{\code{group.by}}{Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class} - \item{split.by}{Name of a metadata column to split plot by; + \item{\code{split.by}}{Name of a metadata column to split plot by; see \code{\link{FetchData}} for more details} - \item{shape.by}{If NULL, all points are circles (default). You can specify any + \item{\code{shape.by}}{If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells} - \item{order}{Specify the order of plotting for the idents. This can be + \item{\code{order}}{Specify the order of plotting for the idents. This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top)} - \item{label}{Whether to label the clusters} - \item{label.size}{Sets size of labels} - \item{repel}{Repel labels} - \item{cells.highlight}{A list of character or numeric vectors of cells to + \item{\code{label}}{Whether to label the clusters} + \item{\code{label.size}}{Sets size of labels} + \item{\code{repel}}{Repel labels} + \item{\code{cells.highlight}}{A list of character or numeric vectors of cells to highlight. If only one group of cells desired, can simply pass a vector instead of a list. If set, colors selected cells to the color(s) in \code{cols.highlight} and other cells black (white if dark.theme = TRUE); will also resize to the size(s) passed to \code{sizes.highlight}} - \item{cols.highlight}{A vector of colors to highlight the cells as; will + \item{\code{cols.highlight}}{A vector of colors to highlight the cells as; will repeat to the length groups in cells.highlight} - \item{sizes.highlight}{Size of highlighted cells; will repeat to the length + \item{\code{sizes.highlight}}{Size of highlighted cells; will repeat to the length groups in cells.highlight} - \item{na.value}{Color value for NA points when using custom scale} - \item{combine}{Combine plots into a single gg object; note that if TRUE; themeing will not work when plotting multiple features} - \item{ncol}{Number of columns for display when combining plots} -}} + \item{\code{na.value}}{Color value for NA points when using custom scale} + \item{\code{combine}}{Combine plots into a single gg object; note that if TRUE; themeing will not work when plotting multiple features} + \item{\code{ncol}}{Number of columns for display when combining plots} + }} } \value{ Returns a DimPlot diff --git a/man/CreateDimReducObject.Rd b/man/CreateDimReducObject.Rd index 7defda9f9..7abd130b9 100644 --- a/man/CreateDimReducObject.Rd +++ b/man/CreateDimReducObject.Rd @@ -5,10 +5,17 @@ \alias{SetDimReduction} \title{Create a DimReduc object} \usage{ -CreateDimReducObject(embeddings = new(Class = "matrix"), - loadings = new(Class = "matrix"), projected = new(Class = "matrix"), - assay = NULL, stdev = numeric(), key = NULL, global = FALSE, - jackstraw = NULL, misc = list()) +CreateDimReducObject( + embeddings = new(Class = "matrix"), + loadings = new(Class = "matrix"), + projected = new(Class = "matrix"), + assay = NULL, + stdev = numeric(), + key = NULL, + global = FALSE, + jackstraw = NULL, + misc = list() +) } \arguments{ \item{embeddings}{A matrix with the cell embeddings} diff --git a/man/CreateGeneActivityMatrix.Rd b/man/CreateGeneActivityMatrix.Rd index 1b4b89b06..d69bc808f 100644 --- a/man/CreateGeneActivityMatrix.Rd +++ b/man/CreateGeneActivityMatrix.Rd @@ -4,9 +4,15 @@ \alias{CreateGeneActivityMatrix} \title{Convert a peak matrix to a gene activity matrix} \usage{ -CreateGeneActivityMatrix(peak.matrix, annotation.file, - seq.levels = c(1:22, "X", "Y"), include.body = TRUE, - upstream = 2000, downstream = 0, verbose = TRUE) +CreateGeneActivityMatrix( + peak.matrix, + annotation.file, + seq.levels = c(1:22, "X", "Y"), + include.body = TRUE, + upstream = 2000, + downstream = 0, + verbose = TRUE +) } \arguments{ \item{peak.matrix}{Matrix of peak counts} diff --git a/man/CreateSeuratObject.Rd b/man/CreateSeuratObject.Rd index 1c3e81e7d..a464b8dc7 100644 --- a/man/CreateSeuratObject.Rd +++ b/man/CreateSeuratObject.Rd @@ -4,9 +4,16 @@ \alias{CreateSeuratObject} \title{Create a Seurat object} \usage{ -CreateSeuratObject(counts, project = "SeuratProject", assay = "RNA", - min.cells = 0, min.features = 0, names.field = 1, - names.delim = "_", meta.data = NULL) +CreateSeuratObject( + counts, + project = "SeuratProject", + assay = "RNA", + min.cells = 0, + min.features = 0, + names.field = 1, + names.delim = "_", + meta.data = NULL +) } \arguments{ \item{counts}{Unnormalized data such as raw counts or TPMs} diff --git a/man/DietSeurat.Rd b/man/DietSeurat.Rd index 558e05d7c..2e6dfb66c 100644 --- a/man/DietSeurat.Rd +++ b/man/DietSeurat.Rd @@ -4,8 +4,16 @@ \alias{DietSeurat} \title{Slim down a Seurat object} \usage{ -DietSeurat(object, counts = TRUE, data = TRUE, scale.data = FALSE, - features = NULL, assays = NULL, dimreducs = NULL, graphs = NULL) +DietSeurat( + object, + counts = TRUE, + data = TRUE, + scale.data = FALSE, + features = NULL, + assays = NULL, + dimreducs = NULL, + graphs = NULL +) } \arguments{ \item{object}{Seurat object} diff --git a/man/DimHeatmap.Rd b/man/DimHeatmap.Rd index 018da2835..c7429b1e7 100644 --- a/man/DimHeatmap.Rd +++ b/man/DimHeatmap.Rd @@ -5,10 +5,23 @@ \alias{PCHeatmap} \title{Dimensional reduction heatmap} \usage{ -DimHeatmap(object, dims = 1, nfeatures = 30, cells = NULL, - reduction = "pca", disp.min = -2.5, disp.max = NULL, - balanced = TRUE, projected = FALSE, ncol = NULL, combine = TRUE, - fast = TRUE, raster = TRUE, slot = "scale.data", assays = NULL) +DimHeatmap( + object, + dims = 1, + nfeatures = 30, + cells = NULL, + reduction = "pca", + disp.min = -2.5, + disp.max = NULL, + balanced = TRUE, + projected = FALSE, + ncol = NULL, + combine = TRUE, + fast = TRUE, + raster = TRUE, + slot = "scale.data", + assays = NULL +) PCHeatmap(object, ...) } diff --git a/man/DimPlot.Rd b/man/DimPlot.Rd index 1bd3889ea..29c9fed17 100644 --- a/man/DimPlot.Rd +++ b/man/DimPlot.Rd @@ -8,12 +8,28 @@ \alias{UMAPPlot} \title{Dimensional reduction plot} \usage{ -DimPlot(object, dims = c(1, 2), cells = NULL, cols = NULL, - pt.size = NULL, reduction = NULL, group.by = NULL, - split.by = NULL, shape.by = NULL, order = NULL, label = FALSE, - label.size = 4, repel = FALSE, cells.highlight = NULL, - cols.highlight = "#DE2D26", sizes.highlight = 1, - na.value = "grey50", combine = TRUE, ncol = NULL, ...) +DimPlot( + object, + dims = c(1, 2), + cells = NULL, + cols = NULL, + pt.size = NULL, + reduction = NULL, + group.by = NULL, + split.by = NULL, + shape.by = NULL, + order = NULL, + label = FALSE, + label.size = 4, + repel = FALSE, + cells.highlight = NULL, + cols.highlight = "#DE2D26", + sizes.highlight = 1, + na.value = "grey50", + combine = TRUE, + ncol = NULL, + ... +) PCAPlot(object, ...) diff --git a/man/DoHeatmap.Rd b/man/DoHeatmap.Rd index 4041f7582..8c5c711bd 100644 --- a/man/DoHeatmap.Rd +++ b/man/DoHeatmap.Rd @@ -4,12 +4,27 @@ \alias{DoHeatmap} \title{Feature expression heatmap} \usage{ -DoHeatmap(object, features = NULL, cells = NULL, group.by = "ident", - group.bar = TRUE, group.colors = NULL, disp.min = -2.5, - disp.max = NULL, slot = "scale.data", assay = NULL, label = TRUE, - size = 5.5, hjust = 0, angle = 45, raster = TRUE, - draw.lines = TRUE, lines.width = NULL, group.bar.height = 0.02, - combine = TRUE) +DoHeatmap( + object, + features = NULL, + cells = NULL, + group.by = "ident", + group.bar = TRUE, + group.colors = NULL, + disp.min = -2.5, + disp.max = NULL, + slot = "scale.data", + assay = NULL, + label = TRUE, + size = 5.5, + hjust = 0, + angle = 45, + raster = TRUE, + draw.lines = TRUE, + lines.width = NULL, + group.bar.height = 0.02, + combine = TRUE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/DotPlot.Rd b/man/DotPlot.Rd index 3a5f10747..eec9138ad 100644 --- a/man/DotPlot.Rd +++ b/man/DotPlot.Rd @@ -5,10 +5,21 @@ \alias{SplitDotPlotGG} \title{Dot plot visualization} \usage{ -DotPlot(object, assay = NULL, features, cols = c("lightgrey", "blue"), - col.min = -2.5, col.max = 2.5, dot.min = 0, dot.scale = 6, - group.by = NULL, split.by = NULL, scale.by = "radius", - scale.min = NA, scale.max = NA) +DotPlot( + object, + assay = NULL, + features, + cols = c("lightgrey", "blue"), + col.min = -2.5, + col.max = 2.5, + dot.min = 0, + dot.scale = 6, + group.by = NULL, + split.by = NULL, + scale.by = "radius", + scale.min = NA, + scale.max = NA +) } \arguments{ \item{object}{Seurat object} diff --git a/man/ExportToCellbrowser.Rd b/man/ExportToCellbrowser.Rd index 11c3a3eff..4796ddf0d 100644 --- a/man/ExportToCellbrowser.Rd +++ b/man/ExportToCellbrowser.Rd @@ -4,11 +4,20 @@ \alias{ExportToCellbrowser} \title{Export Seurat object for UCSC cell browser} \usage{ -ExportToCellbrowser(object, dir, dataset.name = Project(object = object), - reductions = "tsne", markers.file = NULL, - cluster.field = "Cluster", cb.dir = NULL, port = NULL, - skip.expr.matrix = FALSE, skip.metadata = FALSE, - skip.reductions = FALSE, ...) +ExportToCellbrowser( + object, + dir, + dataset.name = Project(object = object), + reductions = "tsne", + markers.file = NULL, + cluster.field = "Cluster", + cb.dir = NULL, + port = NULL, + skip.expr.matrix = FALSE, + skip.metadata = FALSE, + skip.reductions = FALSE, + ... +) } \arguments{ \item{object}{Seurat object} diff --git a/man/FeaturePlot.Rd b/man/FeaturePlot.Rd index ca1eecd55..3e202b085 100644 --- a/man/FeaturePlot.Rd +++ b/man/FeaturePlot.Rd @@ -5,14 +5,32 @@ \alias{FeatureHeatmap} \title{Visualize 'features' on a dimensional reduction plot} \usage{ -FeaturePlot(object, features, dims = c(1, 2), cells = NULL, cols = if - (blend) { c("lightgrey", "#ff0000", "#00ff00") } else { - c("lightgrey", "blue") }, pt.size = NULL, order = FALSE, - min.cutoff = NA, max.cutoff = NA, reduction = NULL, - split.by = NULL, shape.by = NULL, slot = "data", blend = FALSE, - blend.threshold = 0.5, label = FALSE, label.size = 4, - repel = FALSE, ncol = NULL, combine = TRUE, coord.fixed = FALSE, - by.col = TRUE, sort.cell = FALSE) +FeaturePlot( + object, + features, + dims = c(1, 2), + cells = NULL, + cols = if (blend) { c("lightgrey", "#ff0000", "#00ff00") } else { + c("lightgrey", "blue") }, + pt.size = NULL, + order = FALSE, + min.cutoff = NA, + max.cutoff = NA, + reduction = NULL, + split.by = NULL, + shape.by = NULL, + slot = "data", + blend = FALSE, + blend.threshold = 0.5, + label = FALSE, + label.size = 4, + repel = FALSE, + ncol = NULL, + combine = TRUE, + coord.fixed = FALSE, + by.col = TRUE, + sort.cell = FALSE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/FeatureScatter.Rd b/man/FeatureScatter.Rd index 300551ec2..599fcaffb 100644 --- a/man/FeatureScatter.Rd +++ b/man/FeatureScatter.Rd @@ -5,9 +5,19 @@ \alias{GenePlot} \title{Scatter plot of single cell data} \usage{ -FeatureScatter(object, feature1, feature2, cells = NULL, - group.by = NULL, cols = NULL, pt.size = 1, shape.by = NULL, - span = NULL, smooth = FALSE, slot = "data") +FeatureScatter( + object, + feature1, + feature2, + cells = NULL, + group.by = NULL, + cols = NULL, + pt.size = 1, + shape.by = NULL, + span = NULL, + smooth = FALSE, + slot = "data" +) } \arguments{ \item{object}{Seurat object} diff --git a/man/FindAllMarkers.Rd b/man/FindAllMarkers.Rd index 91d1818a7..098ade004 100644 --- a/man/FindAllMarkers.Rd +++ b/man/FindAllMarkers.Rd @@ -5,12 +5,27 @@ \alias{FindAllMarkersNode} \title{Gene expression markers for all identity classes} \usage{ -FindAllMarkers(object, assay = NULL, features = NULL, - logfc.threshold = 0.25, test.use = "wilcox", slot = "data", - min.pct = 0.1, min.diff.pct = -Inf, node = NULL, verbose = TRUE, - only.pos = FALSE, max.cells.per.ident = Inf, random.seed = 1, - latent.vars = NULL, min.cells.feature = 3, min.cells.group = 3, - pseudocount.use = 1, return.thresh = 0.01, ...) +FindAllMarkers( + object, + assay = NULL, + features = NULL, + logfc.threshold = 0.25, + test.use = "wilcox", + slot = "data", + min.pct = 0.1, + min.diff.pct = -Inf, + node = NULL, + verbose = TRUE, + only.pos = FALSE, + max.cells.per.ident = Inf, + random.seed = 1, + latent.vars = NULL, + min.cells.feature = 3, + min.cells.group = 3, + pseudocount.use = 1, + return.thresh = 0.01, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/FindClusters.Rd b/man/FindClusters.Rd index 215109b4d..83f45f22e 100644 --- a/man/FindClusters.Rd +++ b/man/FindClusters.Rd @@ -8,19 +8,44 @@ \usage{ FindClusters(object, ...) -\method{FindClusters}{default}(object, modularity.fxn = 1, - initial.membership = NULL, weights = NULL, node.sizes = NULL, - resolution = 0.8, method = "matrix", algorithm = 1, n.start = 10, - n.iter = 10, random.seed = 0, group.singletons = TRUE, - temp.file.location = NULL, edge.file.name = NULL, verbose = TRUE, - ...) - -\method{FindClusters}{Seurat}(object, graph.name = NULL, - modularity.fxn = 1, initial.membership = NULL, weights = NULL, - node.sizes = NULL, resolution = 0.8, method = "matrix", - algorithm = 1, n.start = 10, n.iter = 10, random.seed = 0, - group.singletons = TRUE, temp.file.location = NULL, - edge.file.name = NULL, verbose = TRUE, ...) +\method{FindClusters}{default}( + object, + modularity.fxn = 1, + initial.membership = NULL, + weights = NULL, + node.sizes = NULL, + resolution = 0.8, + method = "matrix", + algorithm = 1, + n.start = 10, + n.iter = 10, + random.seed = 0, + group.singletons = TRUE, + temp.file.location = NULL, + edge.file.name = NULL, + verbose = TRUE, + ... +) + +\method{FindClusters}{Seurat}( + object, + graph.name = NULL, + modularity.fxn = 1, + initial.membership = NULL, + weights = NULL, + node.sizes = NULL, + resolution = 0.8, + method = "matrix", + algorithm = 1, + n.start = 10, + n.iter = 10, + random.seed = 0, + group.singletons = TRUE, + temp.file.location = NULL, + edge.file.name = NULL, + verbose = TRUE, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/FindConservedMarkers.Rd b/man/FindConservedMarkers.Rd index d1d0798ba..2500454e6 100644 --- a/man/FindConservedMarkers.Rd +++ b/man/FindConservedMarkers.Rd @@ -4,9 +4,17 @@ \alias{FindConservedMarkers} \title{Finds markers that are conserved between the groups} \usage{ -FindConservedMarkers(object, ident.1, ident.2 = NULL, grouping.var, - assay = "RNA", slot = "data", meta.method = minimump, - verbose = TRUE, ...) +FindConservedMarkers( + object, + ident.1, + ident.2 = NULL, + grouping.var, + assay = "RNA", + slot = "data", + meta.method = minimump, + verbose = TRUE, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/FindIntegrationAnchors.Rd b/man/FindIntegrationAnchors.Rd index e6cb48ca1..1d3187985 100644 --- a/man/FindIntegrationAnchors.Rd +++ b/man/FindIntegrationAnchors.Rd @@ -4,13 +4,25 @@ \alias{FindIntegrationAnchors} \title{Find integration anchors} \usage{ -FindIntegrationAnchors(object.list = NULL, assay = NULL, - reference = NULL, anchor.features = 2000, scale = TRUE, +FindIntegrationAnchors( + object.list = NULL, + assay = NULL, + reference = NULL, + anchor.features = 2000, + scale = TRUE, normalization.method = c("LogNormalize", "SCT"), - sct.clip.range = NULL, reduction = c("cca", "rpca"), - l2.norm = TRUE, dims = 1:30, k.anchor = 5, k.filter = 200, - k.score = 30, max.features = 200, nn.method = "rann", eps = 0, - verbose = TRUE) + sct.clip.range = NULL, + reduction = c("cca", "rpca"), + l2.norm = TRUE, + dims = 1:30, + k.anchor = 5, + k.filter = 200, + k.score = 30, + max.features = 200, + nn.method = "rann", + eps = 0, + verbose = TRUE +) } \arguments{ \item{object.list}{A list of objects between which to find anchors for diff --git a/man/FindMarkers.Rd b/man/FindMarkers.Rd index acba420b9..e0b1b02e1 100644 --- a/man/FindMarkers.Rd +++ b/man/FindMarkers.Rd @@ -9,22 +9,53 @@ \usage{ FindMarkers(object, ...) -\method{FindMarkers}{default}(object, slot = "data", - counts = numeric(), cells.1 = NULL, cells.2 = NULL, - features = NULL, reduction = NULL, logfc.threshold = 0.25, - test.use = "wilcox", min.pct = 0.1, min.diff.pct = -Inf, - verbose = TRUE, only.pos = FALSE, max.cells.per.ident = Inf, - random.seed = 1, latent.vars = NULL, min.cells.feature = 3, - min.cells.group = 3, pseudocount.use = 1, ...) - -\method{FindMarkers}{Seurat}(object, ident.1 = NULL, ident.2 = NULL, - group.by = NULL, subset.ident = NULL, assay = NULL, - slot = "data", reduction = NULL, features = NULL, - logfc.threshold = 0.25, test.use = "wilcox", min.pct = 0.1, - min.diff.pct = -Inf, verbose = TRUE, only.pos = FALSE, - max.cells.per.ident = Inf, random.seed = 1, latent.vars = NULL, - min.cells.feature = 3, min.cells.group = 3, pseudocount.use = 1, - ...) +\method{FindMarkers}{default}( + object, + slot = "data", + counts = numeric(), + cells.1 = NULL, + cells.2 = NULL, + features = NULL, + reduction = NULL, + logfc.threshold = 0.25, + test.use = "wilcox", + min.pct = 0.1, + min.diff.pct = -Inf, + verbose = TRUE, + only.pos = FALSE, + max.cells.per.ident = Inf, + random.seed = 1, + latent.vars = NULL, + min.cells.feature = 3, + min.cells.group = 3, + pseudocount.use = 1, + ... +) + +\method{FindMarkers}{Seurat}( + object, + ident.1 = NULL, + ident.2 = NULL, + group.by = NULL, + subset.ident = NULL, + assay = NULL, + slot = "data", + reduction = NULL, + features = NULL, + logfc.threshold = 0.25, + test.use = "wilcox", + min.pct = 0.1, + min.diff.pct = -Inf, + verbose = TRUE, + only.pos = FALSE, + max.cells.per.ident = Inf, + random.seed = 1, + latent.vars = NULL, + min.cells.feature = 3, + min.cells.group = 3, + pseudocount.use = 1, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/FindNeighbors.Rd b/man/FindNeighbors.Rd index 5527f870c..61d15cc1e 100644 --- a/man/FindNeighbors.Rd +++ b/man/FindNeighbors.Rd @@ -10,25 +10,65 @@ \usage{ FindNeighbors(object, ...) -\method{FindNeighbors}{default}(object, distance.matrix = FALSE, - k.param = 20, compute.SNN = TRUE, prune.SNN = 1/15, - nn.method = "rann", annoy.metric = "euclidean", nn.eps = 0, - verbose = TRUE, force.recalc = FALSE, ...) - -\method{FindNeighbors}{Assay}(object, features = NULL, k.param = 20, - compute.SNN = TRUE, prune.SNN = 1/15, nn.method = "rann", - annoy.metric = "euclidean", nn.eps = 0, verbose = TRUE, - force.recalc = FALSE, ...) - -\method{FindNeighbors}{dist}(object, k.param = 20, compute.SNN = TRUE, - prune.SNN = 1/15, nn.method = "rann", annoy.metric = "euclidean", - nn.eps = 0, verbose = TRUE, force.recalc = FALSE, ...) - -\method{FindNeighbors}{Seurat}(object, reduction = "pca", dims = 1:10, - assay = NULL, features = NULL, k.param = 20, compute.SNN = TRUE, - prune.SNN = 1/15, nn.method = "rann", annoy.metric = "euclidean", - nn.eps = 0, verbose = TRUE, force.recalc = FALSE, - do.plot = FALSE, graph.name = NULL, ...) +\method{FindNeighbors}{default}( + object, + distance.matrix = FALSE, + k.param = 20, + compute.SNN = TRUE, + prune.SNN = 1/15, + nn.method = "rann", + annoy.metric = "euclidean", + nn.eps = 0, + verbose = TRUE, + force.recalc = FALSE, + ... +) + +\method{FindNeighbors}{Assay}( + object, + features = NULL, + k.param = 20, + compute.SNN = TRUE, + prune.SNN = 1/15, + nn.method = "rann", + annoy.metric = "euclidean", + nn.eps = 0, + verbose = TRUE, + force.recalc = FALSE, + ... +) + +\method{FindNeighbors}{dist}( + object, + k.param = 20, + compute.SNN = TRUE, + prune.SNN = 1/15, + nn.method = "rann", + annoy.metric = "euclidean", + nn.eps = 0, + verbose = TRUE, + force.recalc = FALSE, + ... +) + +\method{FindNeighbors}{Seurat}( + object, + reduction = "pca", + dims = 1:10, + assay = NULL, + features = NULL, + k.param = 20, + compute.SNN = TRUE, + prune.SNN = 1/15, + nn.method = "rann", + annoy.metric = "euclidean", + nn.eps = 0, + verbose = TRUE, + force.recalc = FALSE, + do.plot = FALSE, + graph.name = NULL, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/FindTransferAnchors.Rd b/man/FindTransferAnchors.Rd index fa9ce247a..7fd5c04af 100644 --- a/man/FindTransferAnchors.Rd +++ b/man/FindTransferAnchors.Rd @@ -4,13 +4,27 @@ \alias{FindTransferAnchors} \title{Find transfer anchors} \usage{ -FindTransferAnchors(reference, query, +FindTransferAnchors( + reference, + query, normalization.method = c("LogNormalize", "SCT"), - reference.assay = NULL, query.assay = NULL, - reduction = "pcaproject", project.query = FALSE, features = NULL, - npcs = 30, l2.norm = TRUE, dims = 1:30, k.anchor = 5, - k.filter = 200, k.score = 30, max.features = 200, - nn.method = "rann", eps = 0, approx.pca = TRUE, verbose = TRUE) + reference.assay = NULL, + query.assay = NULL, + reduction = "pcaproject", + project.query = FALSE, + features = NULL, + npcs = 30, + l2.norm = TRUE, + dims = 1:30, + k.anchor = 5, + k.filter = 200, + k.score = 30, + max.features = 200, + nn.method = "rann", + eps = 0, + approx.pca = TRUE, + verbose = TRUE +) } \arguments{ \item{reference}{Seurat object to use as the reference} diff --git a/man/FindVariableFeatures.Rd b/man/FindVariableFeatures.Rd index ac545ff61..0ae3a8600 100644 --- a/man/FindVariableFeatures.Rd +++ b/man/FindVariableFeatures.Rd @@ -10,24 +10,51 @@ \usage{ FindVariableFeatures(object, ...) -\method{FindVariableFeatures}{default}(object, selection.method = "vst", - loess.span = 0.3, clip.max = "auto", mean.function = FastExpMean, - dispersion.function = FastLogVMR, num.bin = 20, - binning.method = "equal_width", verbose = TRUE, ...) - -\method{FindVariableFeatures}{Assay}(object, selection.method = "vst", - loess.span = 0.3, clip.max = "auto", mean.function = FastExpMean, - dispersion.function = FastLogVMR, num.bin = 20, - binning.method = "equal_width", nfeatures = 2000, - mean.cutoff = c(0.1, 8), dispersion.cutoff = c(1, Inf), - verbose = TRUE, ...) - -\method{FindVariableFeatures}{Seurat}(object, assay = NULL, - selection.method = "vst", loess.span = 0.3, clip.max = "auto", - mean.function = FastExpMean, dispersion.function = FastLogVMR, - num.bin = 20, binning.method = "equal_width", nfeatures = 2000, - mean.cutoff = c(0.1, 8), dispersion.cutoff = c(1, Inf), - verbose = TRUE, ...) +\method{FindVariableFeatures}{default}( + object, + selection.method = "vst", + loess.span = 0.3, + clip.max = "auto", + mean.function = FastExpMean, + dispersion.function = FastLogVMR, + num.bin = 20, + binning.method = "equal_width", + verbose = TRUE, + ... +) + +\method{FindVariableFeatures}{Assay}( + object, + selection.method = "vst", + loess.span = 0.3, + clip.max = "auto", + mean.function = FastExpMean, + dispersion.function = FastLogVMR, + num.bin = 20, + binning.method = "equal_width", + nfeatures = 2000, + mean.cutoff = c(0.1, 8), + dispersion.cutoff = c(1, Inf), + verbose = TRUE, + ... +) + +\method{FindVariableFeatures}{Seurat}( + object, + assay = NULL, + selection.method = "vst", + loess.span = 0.3, + clip.max = "auto", + mean.function = FastExpMean, + dispersion.function = FastLogVMR, + num.bin = 20, + binning.method = "equal_width", + nfeatures = 2000, + mean.cutoff = c(0.1, 8), + dispersion.cutoff = c(1, Inf), + verbose = TRUE, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/GetResidual.Rd b/man/GetResidual.Rd index e8f8a3970..13ef55616 100644 --- a/man/GetResidual.Rd +++ b/man/GetResidual.Rd @@ -4,8 +4,15 @@ \alias{GetResidual} \title{Calculate pearson residuals of features not in the scale.data} \usage{ -GetResidual(object, features, assay = "SCT", umi.assay = "RNA", - clip.range = NULL, replace.value = FALSE, verbose = TRUE) +GetResidual( + object, + features, + assay = "SCT", + umi.assay = "RNA", + clip.range = NULL, + replace.value = FALSE, + verbose = TRUE +) } \arguments{ \item{object}{A seurat object} diff --git a/man/HTODemux.Rd b/man/HTODemux.Rd index 69a097a99..e8c22b7a1 100644 --- a/man/HTODemux.Rd +++ b/man/HTODemux.Rd @@ -4,9 +4,17 @@ \alias{HTODemux} \title{Demultiplex samples based on data from cell 'hashing'} \usage{ -HTODemux(object, assay = "HTO", positive.quantile = 0.99, - init = NULL, nstarts = 100, kfunc = "clara", nsamples = 100, - seed = 42, verbose = TRUE) +HTODemux( + object, + assay = "HTO", + positive.quantile = 0.99, + init = NULL, + nstarts = 100, + kfunc = "clara", + nsamples = 100, + seed = 42, + verbose = TRUE +) } \arguments{ \item{object}{Seurat object. Assumes that the hash tag oligo (HTO) data has been added and normalized.} diff --git a/man/HTOHeatmap.Rd b/man/HTOHeatmap.Rd index 0588fa917..0646ee5d2 100644 --- a/man/HTOHeatmap.Rd +++ b/man/HTOHeatmap.Rd @@ -4,10 +4,15 @@ \alias{HTOHeatmap} \title{Hashtag oligo heatmap} \usage{ -HTOHeatmap(object, assay = "HTO", classification = paste0(assay, - "_classification"), global.classification = paste0(assay, - "_classification.global"), ncells = 5000, singlet.names = NULL, - raster = TRUE) +HTOHeatmap( + object, + assay = "HTO", + classification = paste0(assay, "_classification"), + global.classification = paste0(assay, "_classification.global"), + ncells = 5000, + singlet.names = NULL, + raster = TRUE +) } \arguments{ \item{object}{Seurat object. Assumes that the hash tag oligo (HTO) data has been added and normalized, and demultiplexing has been run with HTODemux().} diff --git a/man/HVFInfo.Rd b/man/HVFInfo.Rd index 36bbda9a5..69e94318b 100644 --- a/man/HVFInfo.Rd +++ b/man/HVFInfo.Rd @@ -10,8 +10,7 @@ HVFInfo(object, ...) \method{HVFInfo}{Assay}(object, selection.method, status = FALSE, ...) -\method{HVFInfo}{Seurat}(object, selection.method = NULL, assay = NULL, - status = FALSE, ...) +\method{HVFInfo}{Seurat}(object, selection.method = NULL, assay = NULL, status = FALSE, ...) } \arguments{ \item{object}{An object} diff --git a/man/Idents.Rd b/man/Idents.Rd index edcf0ffc7..899208d92 100644 --- a/man/Idents.Rd +++ b/man/Idents.Rd @@ -32,11 +32,16 @@ StashIdent(object, save.name, ...) \method{Idents}{Seurat}(object, ...) -\method{Idents}{Seurat}(object, cells = NULL, drop = FALSE, - ...) <- value - -\method{ReorderIdent}{Seurat}(object, var, reverse = FALSE, - afxn = mean, reorder.numeric = FALSE, ...) +\method{Idents}{Seurat}(object, cells = NULL, drop = FALSE, ...) <- value + +\method{ReorderIdent}{Seurat}( + object, + var, + reverse = FALSE, + afxn = mean, + reorder.numeric = FALSE, + ... +) \method{RenameIdents}{Seurat}(object, ...) diff --git a/man/IntegrateData.Rd b/man/IntegrateData.Rd index b90c42575..f05fd4885 100644 --- a/man/IntegrateData.Rd +++ b/man/IntegrateData.Rd @@ -4,11 +4,22 @@ \alias{IntegrateData} \title{Integrate data} \usage{ -IntegrateData(anchorset, new.assay.name = "integrated", - normalization.method = c("LogNormalize", "SCT"), features = NULL, - features.to.integrate = NULL, dims = 1:30, k.weight = 100, - weight.reduction = NULL, sd.weight = 1, sample.tree = NULL, - preserve.order = FALSE, do.cpp = TRUE, eps = 0, verbose = TRUE) +IntegrateData( + anchorset, + new.assay.name = "integrated", + normalization.method = c("LogNormalize", "SCT"), + features = NULL, + features.to.integrate = NULL, + dims = 1:30, + k.weight = 100, + weight.reduction = NULL, + sd.weight = 1, + sample.tree = NULL, + preserve.order = FALSE, + do.cpp = TRUE, + eps = 0, + verbose = TRUE +) } \arguments{ \item{anchorset}{Results from FindIntegrationAnchors} diff --git a/man/JackStraw.Rd b/man/JackStraw.Rd index 2004721b5..285bcad6c 100644 --- a/man/JackStraw.Rd +++ b/man/JackStraw.Rd @@ -4,9 +4,16 @@ \alias{JackStraw} \title{Determine statistical significance of PCA scores.} \usage{ -JackStraw(object, reduction = "pca", assay = NULL, dims = 20, - num.replicate = 100, prop.freq = 0.01, verbose = TRUE, - maxit = 1000) +JackStraw( + object, + reduction = "pca", + assay = NULL, + dims = 20, + num.replicate = 100, + prop.freq = 0.01, + verbose = TRUE, + maxit = 1000 +) } \arguments{ \item{object}{Seurat object} diff --git a/man/JackStrawPlot.Rd b/man/JackStrawPlot.Rd index 0ad06c923..dce058247 100644 --- a/man/JackStrawPlot.Rd +++ b/man/JackStrawPlot.Rd @@ -4,8 +4,7 @@ \alias{JackStrawPlot} \title{JackStraw Plot} \usage{ -JackStrawPlot(object, dims = 1:5, reduction = "pca", xmax = 0.1, - ymax = 0.3) +JackStrawPlot(object, dims = 1:5, reduction = "pca", xmax = 0.1, ymax = 0.3) } \arguments{ \item{object}{Seurat object} diff --git a/man/LabelClusters.Rd b/man/LabelClusters.Rd index d78726196..ba34e2a94 100644 --- a/man/LabelClusters.Rd +++ b/man/LabelClusters.Rd @@ -4,8 +4,15 @@ \alias{LabelClusters} \title{Label clusters on a ggplot2-based scatter plot} \usage{ -LabelClusters(plot, id, clusters = NULL, labels = NULL, - split.by = NULL, repel = TRUE, ...) +LabelClusters( + plot, + id, + clusters = NULL, + labels = NULL, + split.by = NULL, + repel = TRUE, + ... +) } \arguments{ \item{plot}{A ggplot2-based scatter plot} diff --git a/man/LabelPoints.Rd b/man/LabelPoints.Rd index c09231534..7af57e7a6 100644 --- a/man/LabelPoints.Rd +++ b/man/LabelPoints.Rd @@ -5,8 +5,15 @@ \alias{Labeler} \title{Add text labels to a ggplot2 plot} \usage{ -LabelPoints(plot, points, labels = NULL, repel = FALSE, xnudge = 0.3, - ynudge = 0.05, ...) +LabelPoints( + plot, + points, + labels = NULL, + repel = FALSE, + xnudge = 0.3, + ynudge = 0.05, + ... +) } \arguments{ \item{plot}{A ggplot2 plot with a GeomPoint layer} diff --git a/man/Loadings.Rd b/man/Loadings.Rd index 721dbfea8..af4c6547c 100644 --- a/man/Loadings.Rd +++ b/man/Loadings.Rd @@ -14,8 +14,7 @@ Loadings(object, ...) <- value \method{Loadings}{DimReduc}(object, projected = FALSE, ...) -\method{Loadings}{Seurat}(object, reduction = "pca", projected = FALSE, - ...) +\method{Loadings}{Seurat}(object, reduction = "pca", projected = FALSE, ...) \method{Loadings}{DimReduc}(object, projected = TRUE, ...) <- value } diff --git a/man/LocalStruct.Rd b/man/LocalStruct.Rd index 44ffd1e2c..5ced0313b 100644 --- a/man/LocalStruct.Rd +++ b/man/LocalStruct.Rd @@ -4,9 +4,16 @@ \alias{LocalStruct} \title{Calculate the local structure preservation metric} \usage{ -LocalStruct(object, grouping.var, idents = NULL, neighbors = 100, - reduction = "pca", reduced.dims = 1:10, orig.dims = 1:10, - verbose = TRUE) +LocalStruct( + object, + grouping.var, + idents = NULL, + neighbors = 100, + reduction = "pca", + reduced.dims = 1:10, + orig.dims = 1:10, + verbose = TRUE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/MULTIseqDemux.Rd b/man/MULTIseqDemux.Rd index 505cdda59..3b032e144 100644 --- a/man/MULTIseqDemux.Rd +++ b/man/MULTIseqDemux.Rd @@ -4,9 +4,15 @@ \alias{MULTIseqDemux} \title{Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018)} \usage{ -MULTIseqDemux(object, assay = "HTO", quantile = 0.7, - autoThresh = FALSE, maxiter = 5, qrange = seq(from = 0.1, to = 0.9, - by = 0.05), verbose = TRUE) +MULTIseqDemux( + object, + assay = "HTO", + quantile = 0.7, + autoThresh = FALSE, + maxiter = 5, + qrange = seq(from = 0.1, to = 0.9, by = 0.05), + verbose = TRUE +) } \arguments{ \item{object}{Seurat object. Assumes that the specified assay data has been added} diff --git a/man/MetaFeature.Rd b/man/MetaFeature.Rd index 8d7872851..82941cc4d 100644 --- a/man/MetaFeature.Rd +++ b/man/MetaFeature.Rd @@ -4,8 +4,14 @@ \alias{MetaFeature} \title{Aggregate expression of multiple features into a single feature} \usage{ -MetaFeature(object, features, meta.name = "metafeature", cells = NULL, - assay = NULL, slot = "data") +MetaFeature( + object, + features, + meta.name = "metafeature", + cells = NULL, + assay = NULL, + slot = "data" +) } \arguments{ \item{object}{A Seurat object} diff --git a/man/MixingMetric.Rd b/man/MixingMetric.Rd index f9eec617c..a4b3a90f4 100644 --- a/man/MixingMetric.Rd +++ b/man/MixingMetric.Rd @@ -4,8 +4,16 @@ \alias{MixingMetric} \title{Calculates a mixing metric} \usage{ -MixingMetric(object, grouping.var, reduction = "pca", dims = 1:2, - k = 5, max.k = 300, eps = 0, verbose = TRUE) +MixingMetric( + object, + grouping.var, + reduction = "pca", + dims = 1:2, + k = 5, + max.k = 300, + eps = 0, + verbose = TRUE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/NormalizeData.Rd b/man/NormalizeData.Rd index 37d298df5..28cf1e316 100644 --- a/man/NormalizeData.Rd +++ b/man/NormalizeData.Rd @@ -9,17 +9,34 @@ \usage{ NormalizeData(object, ...) -\method{NormalizeData}{default}(object, - normalization.method = "LogNormalize", scale.factor = 10000, - margin = 1, block.size = NULL, verbose = TRUE, ...) +\method{NormalizeData}{default}( + object, + normalization.method = "LogNormalize", + scale.factor = 10000, + margin = 1, + block.size = NULL, + verbose = TRUE, + ... +) -\method{NormalizeData}{Assay}(object, - normalization.method = "LogNormalize", scale.factor = 10000, - margin = 1, verbose = TRUE, ...) +\method{NormalizeData}{Assay}( + object, + normalization.method = "LogNormalize", + scale.factor = 10000, + margin = 1, + verbose = TRUE, + ... +) -\method{NormalizeData}{Seurat}(object, assay = NULL, - normalization.method = "LogNormalize", scale.factor = 10000, - margin = 1, verbose = TRUE, ...) +\method{NormalizeData}{Seurat}( + object, + assay = NULL, + normalization.method = "LogNormalize", + scale.factor = 10000, + margin = 1, + verbose = TRUE, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/OldWhichCells.Rd b/man/OldWhichCells.Rd index 32607c37b..8968df339 100644 --- a/man/OldWhichCells.Rd +++ b/man/OldWhichCells.Rd @@ -8,14 +8,30 @@ \usage{ OldWhichCells(object, ...) -\method{OldWhichCells}{Assay}(object, cells, subset.name = NULL, - low.threshold = -Inf, high.threshold = Inf, accept.value = NULL, - ...) +\method{OldWhichCells}{Assay}( + object, + cells, + subset.name = NULL, + low.threshold = -Inf, + high.threshold = Inf, + accept.value = NULL, + ... +) -\method{OldWhichCells}{Seurat}(object, cells = NULL, - subset.name = NULL, low.threshold = -Inf, high.threshold = Inf, - accept.value = NULL, ident.keep = NULL, ident.remove = NULL, - max.cells.per.ident = Inf, random.seed = 1, assay = NULL, ...) +\method{OldWhichCells}{Seurat}( + object, + cells = NULL, + subset.name = NULL, + low.threshold = -Inf, + high.threshold = Inf, + accept.value = NULL, + ident.keep = NULL, + ident.remove = NULL, + max.cells.per.ident = Inf, + random.seed = 1, + assay = NULL, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/PCASigGenes.Rd b/man/PCASigGenes.Rd index 70ac592e0..1d6d9b459 100644 --- a/man/PCASigGenes.Rd +++ b/man/PCASigGenes.Rd @@ -4,8 +4,13 @@ \alias{PCASigGenes} \title{Significant genes from a PCA} \usage{ -PCASigGenes(object, pcs.use, pval.cut = 0.1, use.full = FALSE, - max.per.pc = NULL) +PCASigGenes( + object, + pcs.use, + pval.cut = 0.1, + use.full = FALSE, + max.per.pc = NULL +) } \arguments{ \item{object}{Seurat object} diff --git a/man/PercentageFeatureSet.Rd b/man/PercentageFeatureSet.Rd index 7fad70050..23a0352c9 100644 --- a/man/PercentageFeatureSet.Rd +++ b/man/PercentageFeatureSet.Rd @@ -4,8 +4,13 @@ \alias{PercentageFeatureSet} \title{Calculate the percentage of all counts that belong to a given set of features} \usage{ -PercentageFeatureSet(object, pattern = NULL, features = NULL, - col.name = NULL, assay = NULL) +PercentageFeatureSet( + object, + pattern = NULL, + features = NULL, + col.name = NULL, + assay = NULL +) } \arguments{ \item{object}{A Seurat object} diff --git a/man/PolyDimPlot.Rd b/man/PolyDimPlot.Rd index b6832bad1..a72c51311 100644 --- a/man/PolyDimPlot.Rd +++ b/man/PolyDimPlot.Rd @@ -4,8 +4,13 @@ \alias{PolyDimPlot} \title{Polygon DimPlot} \usage{ -PolyDimPlot(object, group.by = NULL, cells = NULL, - poly.data = "spatial", flip.coords = FALSE) +PolyDimPlot( + object, + group.by = NULL, + cells = NULL, + poly.data = "spatial", + flip.coords = FALSE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/PolyFeaturePlot.Rd b/man/PolyFeaturePlot.Rd index 0e8e33b14..ba48d100a 100644 --- a/man/PolyFeaturePlot.Rd +++ b/man/PolyFeaturePlot.Rd @@ -4,9 +4,17 @@ \alias{PolyFeaturePlot} \title{Polygon FeaturePlot} \usage{ -PolyFeaturePlot(object, features, cells = NULL, poly.data = "spatial", - ncol = ceiling(x = length(x = features)/2), min.cutoff = 0, - max.cutoff = NA, common.scale = TRUE, flip.coords = FALSE) +PolyFeaturePlot( + object, + features, + cells = NULL, + poly.data = "spatial", + ncol = ceiling(x = length(x = features)/2), + min.cutoff = 0, + max.cutoff = NA, + common.scale = TRUE, + flip.coords = FALSE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/PrepSCTIntegration.Rd b/man/PrepSCTIntegration.Rd index 081d6e766..a0545766a 100644 --- a/man/PrepSCTIntegration.Rd +++ b/man/PrepSCTIntegration.Rd @@ -4,8 +4,13 @@ \alias{PrepSCTIntegration} \title{Prepare an object list that has been run through SCTransform for integration} \usage{ -PrepSCTIntegration(object.list, assay = NULL, anchor.features = 2000, - sct.clip.range = NULL, verbose = TRUE) +PrepSCTIntegration( + object.list, + assay = NULL, + anchor.features = 2000, + sct.clip.range = NULL, + verbose = TRUE +) } \arguments{ \item{object.list}{A list of objects to prep for integration} diff --git a/man/ProjectDim.Rd b/man/ProjectDim.Rd index 6d1210624..5b8307341 100644 --- a/man/ProjectDim.Rd +++ b/man/ProjectDim.Rd @@ -4,9 +4,16 @@ \alias{ProjectDim} \title{Project Dimensional reduction onto full dataset} \usage{ -ProjectDim(object, reduction = "pca", assay = NULL, dims.print = 1:5, - nfeatures.print = 20, overwrite = FALSE, do.center = FALSE, - verbose = TRUE) +ProjectDim( + object, + reduction = "pca", + assay = NULL, + dims.print = 1:5, + nfeatures.print = 20, + overwrite = FALSE, + do.center = FALSE, + verbose = TRUE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/RenameCells.Rd b/man/RenameCells.Rd index e3e0c3929..8a071cf75 100644 --- a/man/RenameCells.Rd +++ b/man/RenameCells.Rd @@ -13,8 +13,13 @@ RenameCells(object, ...) \method{RenameCells}{DimReduc}(object, new.names = NULL, ...) -\method{RenameCells}{Seurat}(object, add.cell.id = NULL, - new.names = NULL, for.merge = FALSE, ...) +\method{RenameCells}{Seurat}( + object, + add.cell.id = NULL, + new.names = NULL, + for.merge = FALSE, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/RidgePlot.Rd b/man/RidgePlot.Rd index 491e7929d..2bba82d6c 100644 --- a/man/RidgePlot.Rd +++ b/man/RidgePlot.Rd @@ -4,9 +4,22 @@ \alias{RidgePlot} \title{Single cell ridge plot} \usage{ -RidgePlot(object, features, cols = NULL, idents = NULL, sort = FALSE, - assay = NULL, group.by = NULL, y.max = NULL, same.y.lims = FALSE, - log = FALSE, ncol = NULL, combine = TRUE, slot = "data", ...) +RidgePlot( + object, + features, + cols = NULL, + idents = NULL, + sort = FALSE, + assay = NULL, + group.by = NULL, + y.max = NULL, + same.y.lims = FALSE, + log = FALSE, + ncol = NULL, + combine = TRUE, + slot = "data", + ... +) } \arguments{ \item{object}{Seurat object} diff --git a/man/RunALRA.Rd b/man/RunALRA.Rd index 8ad711ad0..ac7106ef8 100644 --- a/man/RunALRA.Rd +++ b/man/RunALRA.Rd @@ -8,14 +8,34 @@ \usage{ RunALRA(object, ...) -\method{RunALRA}{default}(object, k = NULL, q = 10, - quantile.prob = 0.001, use.mkl = FALSE, mkl.seed = -1, ...) - -\method{RunALRA}{Seurat}(object, k = NULL, q = 10, - quantile.prob = 0.001, use.mkl = FALSE, mkl.seed = -1, - assay = NULL, slot = "data", setDefaultAssay = TRUE, - genes.use = NULL, K = NULL, thresh = 6, noise.start = NULL, - q.k = 2, k.only = FALSE, ...) +\method{RunALRA}{default}( + object, + k = NULL, + q = 10, + quantile.prob = 0.001, + use.mkl = FALSE, + mkl.seed = -1, + ... +) + +\method{RunALRA}{Seurat}( + object, + k = NULL, + q = 10, + quantile.prob = 0.001, + use.mkl = FALSE, + mkl.seed = -1, + assay = NULL, + slot = "data", + setDefaultAssay = TRUE, + genes.use = NULL, + K = NULL, + thresh = 6, + noise.start = NULL, + q.k = 2, + k.only = FALSE, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/RunCCA.Rd b/man/RunCCA.Rd index ead5c6842..5e6cffcd3 100644 --- a/man/RunCCA.Rd +++ b/man/RunCCA.Rd @@ -8,13 +8,31 @@ \usage{ RunCCA(object1, object2, ...) -\method{RunCCA}{default}(object1, object2, standardize = TRUE, - num.cc = 20, seed.use = 42, verbose = FALSE, ...) +\method{RunCCA}{default}( + object1, + object2, + standardize = TRUE, + num.cc = 20, + seed.use = 42, + verbose = FALSE, + ... +) -\method{RunCCA}{Seurat}(object1, object2, assay1 = NULL, assay2 = NULL, - num.cc = 20, features = NULL, renormalize = FALSE, - rescale = FALSE, compute.gene.loadings = TRUE, add.cell.id1 = NULL, - add.cell.id2 = NULL, verbose = TRUE, ...) +\method{RunCCA}{Seurat}( + object1, + object2, + assay1 = NULL, + assay2 = NULL, + num.cc = 20, + features = NULL, + renormalize = FALSE, + rescale = FALSE, + compute.gene.loadings = TRUE, + add.cell.id1 = NULL, + add.cell.id2 = NULL, + verbose = TRUE, + ... +) } \arguments{ \item{object1}{First Seurat object} diff --git a/man/RunICA.Rd b/man/RunICA.Rd index 942c7834b..cb1569a4f 100644 --- a/man/RunICA.Rd +++ b/man/RunICA.Rd @@ -9,20 +9,52 @@ \usage{ RunICA(object, ...) -\method{RunICA}{default}(object, assay = NULL, nics = 50, - rev.ica = FALSE, ica.function = "icafast", verbose = TRUE, - ndims.print = 1:5, nfeatures.print = 30, reduction.name = "ica", - reduction.key = "ica_", seed.use = 42, ...) - -\method{RunICA}{Assay}(object, assay = NULL, features = NULL, - nics = 50, rev.ica = FALSE, ica.function = "icafast", - verbose = TRUE, ndims.print = 1:5, nfeatures.print = 30, - reduction.name = "ica", reduction.key = "ica_", seed.use = 42, ...) - -\method{RunICA}{Seurat}(object, assay = NULL, features = NULL, - nics = 50, rev.ica = FALSE, ica.function = "icafast", - verbose = TRUE, ndims.print = 1:5, nfeatures.print = 30, - reduction.name = "ica", reduction.key = "IC_", seed.use = 42, ...) +\method{RunICA}{default}( + object, + assay = NULL, + nics = 50, + rev.ica = FALSE, + ica.function = "icafast", + verbose = TRUE, + ndims.print = 1:5, + nfeatures.print = 30, + reduction.name = "ica", + reduction.key = "ica_", + seed.use = 42, + ... +) + +\method{RunICA}{Assay}( + object, + assay = NULL, + features = NULL, + nics = 50, + rev.ica = FALSE, + ica.function = "icafast", + verbose = TRUE, + ndims.print = 1:5, + nfeatures.print = 30, + reduction.name = "ica", + reduction.key = "ica_", + seed.use = 42, + ... +) + +\method{RunICA}{Seurat}( + object, + assay = NULL, + features = NULL, + nics = 50, + rev.ica = FALSE, + ica.function = "icafast", + verbose = TRUE, + ndims.print = 1:5, + nfeatures.print = 30, + reduction.name = "ica", + reduction.key = "IC_", + seed.use = 42, + ... +) } \arguments{ \item{object}{Seurat object} diff --git a/man/RunLSI.Rd b/man/RunLSI.Rd index 391a59bc4..61efcaf2e 100644 --- a/man/RunLSI.Rd +++ b/man/RunLSI.Rd @@ -9,16 +9,39 @@ \usage{ RunLSI(object, ...) -\method{RunLSI}{default}(object, assay = NULL, n = 50, - reduction.key = "LSI_", scale.max = NULL, seed.use = 42, - verbose = TRUE, ...) +\method{RunLSI}{default}( + object, + assay = NULL, + n = 50, + reduction.key = "LSI_", + scale.max = NULL, + seed.use = 42, + verbose = TRUE, + ... +) -\method{RunLSI}{Assay}(object, assay = NULL, features = NULL, n = 50, - reduction.key = "LSI_", scale.max = NULL, verbose = TRUE, ...) +\method{RunLSI}{Assay}( + object, + assay = NULL, + features = NULL, + n = 50, + reduction.key = "LSI_", + scale.max = NULL, + verbose = TRUE, + ... +) -\method{RunLSI}{Seurat}(object, assay = NULL, features = NULL, - n = 50, reduction.key = "LSI_", reduction.name = "lsi", - scale.max = NULL, verbose = TRUE, ...) +\method{RunLSI}{Seurat}( + object, + assay = NULL, + features = NULL, + n = 50, + reduction.key = "LSI_", + reduction.name = "lsi", + scale.max = NULL, + verbose = TRUE, + ... +) } \arguments{ \item{object}{Seurat object} diff --git a/man/RunPCA.Rd b/man/RunPCA.Rd index d0a20d149..c5aecfb52 100644 --- a/man/RunPCA.Rd +++ b/man/RunPCA.Rd @@ -9,20 +9,51 @@ \usage{ RunPCA(object, ...) -\method{RunPCA}{default}(object, assay = NULL, npcs = 50, - rev.pca = FALSE, weight.by.var = TRUE, verbose = TRUE, - ndims.print = 1:5, nfeatures.print = 30, reduction.key = "PC_", - seed.use = 42, approx = TRUE, ...) - -\method{RunPCA}{Assay}(object, assay = NULL, features = NULL, - npcs = 50, rev.pca = FALSE, weight.by.var = TRUE, verbose = TRUE, - ndims.print = 1:5, nfeatures.print = 30, reduction.key = "PC_", - seed.use = 42, ...) - -\method{RunPCA}{Seurat}(object, assay = NULL, features = NULL, - npcs = 50, rev.pca = FALSE, weight.by.var = TRUE, verbose = TRUE, - ndims.print = 1:5, nfeatures.print = 30, reduction.name = "pca", - reduction.key = "PC_", seed.use = 42, ...) +\method{RunPCA}{default}( + object, + assay = NULL, + npcs = 50, + rev.pca = FALSE, + weight.by.var = TRUE, + verbose = TRUE, + ndims.print = 1:5, + nfeatures.print = 30, + reduction.key = "PC_", + seed.use = 42, + approx = TRUE, + ... +) + +\method{RunPCA}{Assay}( + object, + assay = NULL, + features = NULL, + npcs = 50, + rev.pca = FALSE, + weight.by.var = TRUE, + verbose = TRUE, + ndims.print = 1:5, + nfeatures.print = 30, + reduction.key = "PC_", + seed.use = 42, + ... +) + +\method{RunPCA}{Seurat}( + object, + assay = NULL, + features = NULL, + npcs = 50, + rev.pca = FALSE, + weight.by.var = TRUE, + verbose = TRUE, + ndims.print = 1:5, + nfeatures.print = 30, + reduction.name = "pca", + reduction.key = "PC_", + seed.use = 42, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/RunTSNE.Rd b/man/RunTSNE.Rd index 8da749669..34136f686 100644 --- a/man/RunTSNE.Rd +++ b/man/RunTSNE.Rd @@ -10,22 +10,55 @@ \usage{ RunTSNE(object, ...) -\method{RunTSNE}{matrix}(object, assay = NULL, seed.use = 1, - tsne.method = "Rtsne", add.iter = 0, dim.embed = 2, - reduction.key = "tSNE_", ...) - -\method{RunTSNE}{DimReduc}(object, cells = NULL, dims = 1:5, - seed.use = 1, tsne.method = "Rtsne", add.iter = 0, dim.embed = 2, - reduction.key = "tSNE_", ...) - -\method{RunTSNE}{dist}(object, assay = NULL, seed.use = 1, - tsne.method = "Rtsne", add.iter = 0, dim.embed = 2, - reduction.key = "tSNE_", ...) - -\method{RunTSNE}{Seurat}(object, reduction = "pca", cells = NULL, - dims = 1:5, features = NULL, seed.use = 1, tsne.method = "Rtsne", - add.iter = 0, dim.embed = 2, distance.matrix = NULL, - reduction.name = "tsne", reduction.key = "tSNE_", ...) +\method{RunTSNE}{matrix}( + object, + assay = NULL, + seed.use = 1, + tsne.method = "Rtsne", + add.iter = 0, + dim.embed = 2, + reduction.key = "tSNE_", + ... +) + +\method{RunTSNE}{DimReduc}( + object, + cells = NULL, + dims = 1:5, + seed.use = 1, + tsne.method = "Rtsne", + add.iter = 0, + dim.embed = 2, + reduction.key = "tSNE_", + ... +) + +\method{RunTSNE}{dist}( + object, + assay = NULL, + seed.use = 1, + tsne.method = "Rtsne", + add.iter = 0, + dim.embed = 2, + reduction.key = "tSNE_", + ... +) + +\method{RunTSNE}{Seurat}( + object, + reduction = "pca", + cells = NULL, + dims = 1:5, + features = NULL, + seed.use = 1, + tsne.method = "Rtsne", + add.iter = 0, + dim.embed = 2, + distance.matrix = NULL, + reduction.name = "tsne", + reduction.key = "tSNE_", + ... +) } \arguments{ \item{object}{Seurat object} diff --git a/man/RunUMAP.Rd b/man/RunUMAP.Rd index 8014d96ad..bab8bdc64 100644 --- a/man/RunUMAP.Rd +++ b/man/RunUMAP.Rd @@ -9,33 +9,84 @@ \usage{ RunUMAP(object, ...) -\method{RunUMAP}{default}(object, assay = NULL, umap.method = "uwot", - n.neighbors = 30L, n.components = 2L, metric = "cosine", - n.epochs = NULL, learning.rate = 1, min.dist = 0.3, spread = 1, - set.op.mix.ratio = 1, local.connectivity = 1L, - repulsion.strength = 1, negative.sample.rate = 5, a = NULL, - b = NULL, uwot.sgd = FALSE, seed.use = 42, metric.kwds = NULL, - angular.rp.forest = FALSE, reduction.key = "UMAP_", verbose = TRUE, - ...) - -\method{RunUMAP}{Graph}(object, assay = NULL, - umap.method = "umap-learn", n.components = 2L, - metric = "correlation", n.epochs = 0L, learning.rate = 1, - min.dist = 0.3, spread = 1, repulsion.strength = 1, - negative.sample.rate = 5L, a = NULL, b = NULL, uwot.sgd = FALSE, - seed.use = 42L, metric.kwds = NULL, verbose = TRUE, - reduction.key = "UMAP_", ...) - -\method{RunUMAP}{Seurat}(object, dims = NULL, reduction = "pca", - features = NULL, graph = NULL, assay = "RNA", - umap.method = "uwot", n.neighbors = 30L, n.components = 2L, - metric = "cosine", n.epochs = NULL, learning.rate = 1, - min.dist = 0.3, spread = 1, set.op.mix.ratio = 1, - local.connectivity = 1L, repulsion.strength = 1, - negative.sample.rate = 5L, a = NULL, b = NULL, uwot.sgd = FALSE, - seed.use = 42L, metric.kwds = NULL, angular.rp.forest = FALSE, - verbose = TRUE, reduction.name = "umap", reduction.key = "UMAP_", - ...) +\method{RunUMAP}{default}( + object, + assay = NULL, + umap.method = "uwot", + n.neighbors = 30L, + n.components = 2L, + metric = "cosine", + n.epochs = NULL, + learning.rate = 1, + min.dist = 0.3, + spread = 1, + set.op.mix.ratio = 1, + local.connectivity = 1L, + repulsion.strength = 1, + negative.sample.rate = 5, + a = NULL, + b = NULL, + uwot.sgd = FALSE, + seed.use = 42, + metric.kwds = NULL, + angular.rp.forest = FALSE, + reduction.key = "UMAP_", + verbose = TRUE, + ... +) + +\method{RunUMAP}{Graph}( + object, + assay = NULL, + umap.method = "umap-learn", + n.components = 2L, + metric = "correlation", + n.epochs = 0L, + learning.rate = 1, + min.dist = 0.3, + spread = 1, + repulsion.strength = 1, + negative.sample.rate = 5L, + a = NULL, + b = NULL, + uwot.sgd = FALSE, + seed.use = 42L, + metric.kwds = NULL, + verbose = TRUE, + reduction.key = "UMAP_", + ... +) + +\method{RunUMAP}{Seurat}( + object, + dims = NULL, + reduction = "pca", + features = NULL, + graph = NULL, + assay = "RNA", + umap.method = "uwot", + n.neighbors = 30L, + n.components = 2L, + metric = "cosine", + n.epochs = NULL, + learning.rate = 1, + min.dist = 0.3, + spread = 1, + set.op.mix.ratio = 1, + local.connectivity = 1L, + repulsion.strength = 1, + negative.sample.rate = 5L, + a = NULL, + b = NULL, + uwot.sgd = FALSE, + seed.use = 42L, + metric.kwds = NULL, + angular.rp.forest = FALSE, + verbose = TRUE, + reduction.name = "umap", + reduction.key = "UMAP_", + ... +) } \arguments{ \item{object}{An object} diff --git a/man/SCTransform.Rd b/man/SCTransform.Rd index c06c21394..03a211e2c 100644 --- a/man/SCTransform.Rd +++ b/man/SCTransform.Rd @@ -4,13 +4,25 @@ \alias{SCTransform} \title{Use regularized negative binomial regression to normalize UMI count data} \usage{ -SCTransform(object, assay = "RNA", new.assay.name = "SCT", - do.correct.umi = TRUE, ncells = NULL, variable.features.n = 3000, - variable.features.rv.th = 1.3, vars.to.regress = NULL, - do.scale = FALSE, do.center = TRUE, clip.range = c(-sqrt(x = ncol(x - = object[[assay]])/30), sqrt(x = ncol(x = object[[assay]])/30)), - conserve.memory = FALSE, return.only.var.genes = TRUE, - seed.use = 1448145, verbose = TRUE, ...) +SCTransform( + object, + assay = "RNA", + new.assay.name = "SCT", + do.correct.umi = TRUE, + ncells = NULL, + variable.features.n = 3000, + variable.features.rv.th = 1.3, + vars.to.regress = NULL, + do.scale = FALSE, + do.center = TRUE, + clip.range = c(-sqrt(x = ncol(x = object[[assay]])/30), sqrt(x = ncol(x = + object[[assay]])/30)), + conserve.memory = FALSE, + return.only.var.genes = TRUE, + seed.use = 1448145, + verbose = TRUE, + ... +) } \arguments{ \item{object}{A seurat object} diff --git a/man/ScaleData.Rd b/man/ScaleData.Rd index 8b311d755..d39e0791c 100644 --- a/man/ScaleData.Rd +++ b/man/ScaleData.Rd @@ -9,23 +9,56 @@ \usage{ ScaleData(object, ...) -\method{ScaleData}{default}(object, features = NULL, - vars.to.regress = NULL, latent.data = NULL, split.by = NULL, - model.use = "linear", use.umi = FALSE, do.scale = TRUE, - do.center = TRUE, scale.max = 10, block.size = 1000, - min.cells.to.block = 3000, verbose = TRUE, ...) - -\method{ScaleData}{Assay}(object, features = NULL, - vars.to.regress = NULL, latent.data = NULL, split.by = NULL, - model.use = "linear", use.umi = FALSE, do.scale = TRUE, - do.center = TRUE, scale.max = 10, block.size = 1000, - min.cells.to.block = 3000, verbose = TRUE, ...) - -\method{ScaleData}{Seurat}(object, features = NULL, assay = NULL, - vars.to.regress = NULL, split.by = NULL, model.use = "linear", - use.umi = FALSE, do.scale = TRUE, do.center = TRUE, - scale.max = 10, block.size = 1000, min.cells.to.block = 3000, - verbose = TRUE, ...) +\method{ScaleData}{default}( + object, + features = NULL, + vars.to.regress = NULL, + latent.data = NULL, + split.by = NULL, + model.use = "linear", + use.umi = FALSE, + do.scale = TRUE, + do.center = TRUE, + scale.max = 10, + block.size = 1000, + min.cells.to.block = 3000, + verbose = TRUE, + ... +) + +\method{ScaleData}{Assay}( + object, + features = NULL, + vars.to.regress = NULL, + latent.data = NULL, + split.by = NULL, + model.use = "linear", + use.umi = FALSE, + do.scale = TRUE, + do.center = TRUE, + scale.max = 10, + block.size = 1000, + min.cells.to.block = 3000, + verbose = TRUE, + ... +) + +\method{ScaleData}{Seurat}( + object, + features = NULL, + assay = NULL, + vars.to.regress = NULL, + split.by = NULL, + model.use = "linear", + use.umi = FALSE, + do.scale = TRUE, + do.center = TRUE, + scale.max = 10, + block.size = 1000, + min.cells.to.block = 3000, + verbose = TRUE, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/ScoreJackStraw.Rd b/man/ScoreJackStraw.Rd index 1cf1713cf..5be895815 100644 --- a/man/ScoreJackStraw.Rd +++ b/man/ScoreJackStraw.Rd @@ -9,14 +9,18 @@ \usage{ ScoreJackStraw(object, ...) -\method{ScoreJackStraw}{JackStrawData}(object, dims = 1:5, - score.thresh = 1e-05, ...) - -\method{ScoreJackStraw}{DimReduc}(object, dims = 1:5, - score.thresh = 1e-05, ...) - -\method{ScoreJackStraw}{Seurat}(object, reduction = "pca", dims = 1:5, - score.thresh = 1e-05, do.plot = FALSE, ...) +\method{ScoreJackStraw}{JackStrawData}(object, dims = 1:5, score.thresh = 1e-05, ...) + +\method{ScoreJackStraw}{DimReduc}(object, dims = 1:5, score.thresh = 1e-05, ...) + +\method{ScoreJackStraw}{Seurat}( + object, + reduction = "pca", + dims = 1:5, + score.thresh = 1e-05, + do.plot = FALSE, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/SelectIntegrationFeatures.Rd b/man/SelectIntegrationFeatures.Rd index 6dac1227e..1ecaf2f2b 100644 --- a/man/SelectIntegrationFeatures.Rd +++ b/man/SelectIntegrationFeatures.Rd @@ -4,8 +4,14 @@ \alias{SelectIntegrationFeatures} \title{Select integration features} \usage{ -SelectIntegrationFeatures(object.list, nfeatures = 2000, assay = NULL, - verbose = TRUE, fvf.nfeatures = 2000, ...) +SelectIntegrationFeatures( + object.list, + nfeatures = 2000, + assay = NULL, + verbose = TRUE, + fvf.nfeatures = 2000, + ... +) } \arguments{ \item{object.list}{List of seurat objects} diff --git a/man/SetAssayData.Rd b/man/SetAssayData.Rd index c2d7c4a0f..cdff1a931 100644 --- a/man/SetAssayData.Rd +++ b/man/SetAssayData.Rd @@ -10,8 +10,7 @@ SetAssayData(object, ...) \method{SetAssayData}{Assay}(object, slot, new.data, ...) -\method{SetAssayData}{Seurat}(object, slot = "data", new.data, - assay = NULL, ...) +\method{SetAssayData}{Seurat}(object, slot = "data", new.data, assay = NULL, ...) } \arguments{ \item{object}{An object} diff --git a/man/SeuratTheme.Rd b/man/SeuratTheme.Rd index 5e9a62606..b4169a400 100644 --- a/man/SeuratTheme.Rd +++ b/man/SeuratTheme.Rd @@ -19,8 +19,14 @@ SeuratTheme() DarkTheme(...) -FontSize(x.text = NULL, y.text = NULL, x.title = NULL, - y.title = NULL, main = NULL, ...) +FontSize( + x.text = NULL, + y.text = NULL, + x.title = NULL, + y.title = NULL, + main = NULL, + ... +) NoAxes(..., keep.text = FALSE, keep.ticks = FALSE) diff --git a/man/SubsetData.Rd b/man/SubsetData.Rd index 10d427f89..a590bf6c8 100644 --- a/man/SubsetData.Rd +++ b/man/SubsetData.Rd @@ -8,14 +8,30 @@ \usage{ SubsetData(object, ...) -\method{SubsetData}{Assay}(object, cells = NULL, subset.name = NULL, - low.threshold = -Inf, high.threshold = Inf, accept.value = NULL, - ...) +\method{SubsetData}{Assay}( + object, + cells = NULL, + subset.name = NULL, + low.threshold = -Inf, + high.threshold = Inf, + accept.value = NULL, + ... +) -\method{SubsetData}{Seurat}(object, assay = NULL, cells = NULL, - subset.name = NULL, ident.use = NULL, ident.remove = NULL, - low.threshold = -Inf, high.threshold = Inf, accept.value = NULL, - max.cells.per.ident = Inf, random.seed = 1, ...) +\method{SubsetData}{Seurat}( + object, + assay = NULL, + cells = NULL, + subset.name = NULL, + ident.use = NULL, + ident.remove = NULL, + low.threshold = -Inf, + high.threshold = Inf, + accept.value = NULL, + max.cells.per.ident = Inf, + random.seed = 1, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/TopFeatures.Rd b/man/TopFeatures.Rd index 036bf57ef..52319b479 100644 --- a/man/TopFeatures.Rd +++ b/man/TopFeatures.Rd @@ -4,8 +4,14 @@ \alias{TopFeatures} \title{Find features with highest scores for a given dimensional reduction technique} \usage{ -TopFeatures(object, dim = 1, nfeatures = 20, projected = FALSE, - balanced = FALSE, ...) +TopFeatures( + object, + dim = 1, + nfeatures = 20, + projected = FALSE, + balanced = FALSE, + ... +) } \arguments{ \item{object}{DimReduc object} diff --git a/man/TransferData.Rd b/man/TransferData.Rd index d6b5af28e..1388696f9 100644 --- a/man/TransferData.Rd +++ b/man/TransferData.Rd @@ -4,9 +4,19 @@ \alias{TransferData} \title{Transfer Labels} \usage{ -TransferData(anchorset, refdata, weight.reduction = "pcaproject", - l2.norm = FALSE, dims = 1:30, k.weight = 50, sd.weight = 1, - eps = 0, do.cpp = TRUE, verbose = TRUE, slot = "data") +TransferData( + anchorset, + refdata, + weight.reduction = "pcaproject", + l2.norm = FALSE, + dims = 1:30, + k.weight = 50, + sd.weight = 1, + eps = 0, + do.cpp = TRUE, + verbose = TRUE, + slot = "data" +) } \arguments{ \item{anchorset}{Results from FindTransferAnchors} diff --git a/man/UpdateSymbolList.Rd b/man/UpdateSymbolList.Rd index 58d378599..aca1e2339 100644 --- a/man/UpdateSymbolList.Rd +++ b/man/UpdateSymbolList.Rd @@ -8,11 +8,21 @@ \url{https://www.genenames.org/} \url{http://rest.genenames.org/} } \usage{ -GeneSymbolThesarus(symbols, timeout = 10, several.ok = FALSE, - verbose = TRUE, ...) +GeneSymbolThesarus( + symbols, + timeout = 10, + several.ok = FALSE, + verbose = TRUE, + ... +) -UpdateSymbolList(symbols, timeout = 10, several.ok = FALSE, - verbose = TRUE, ...) +UpdateSymbolList( + symbols, + timeout = 10, + several.ok = FALSE, + verbose = TRUE, + ... +) } \arguments{ \item{symbols}{A vector of gene symbols} diff --git a/man/VariableFeaturePlot.Rd b/man/VariableFeaturePlot.Rd index fbb419045..08f15ae1a 100644 --- a/man/VariableFeaturePlot.Rd +++ b/man/VariableFeaturePlot.Rd @@ -6,8 +6,14 @@ \alias{MeanVarPlot} \title{View variable features} \usage{ -VariableFeaturePlot(object, cols = c("black", "red"), pt.size = 1, - log = NULL, selection.method = NULL, assay = NULL) +VariableFeaturePlot( + object, + cols = c("black", "red"), + pt.size = 1, + log = NULL, + selection.method = NULL, + assay = NULL +) } \arguments{ \item{object}{Seurat object} diff --git a/man/VariableFeatures.Rd b/man/VariableFeatures.Rd index f42a1da34..064e84923 100644 --- a/man/VariableFeatures.Rd +++ b/man/VariableFeatures.Rd @@ -15,8 +15,7 @@ VariableFeatures(object, ...) <- value \method{VariableFeatures}{Assay}(object, selection.method = NULL, ...) -\method{VariableFeatures}{Seurat}(object, assay = NULL, - selection.method = NULL, ...) +\method{VariableFeatures}{Seurat}(object, assay = NULL, selection.method = NULL, ...) \method{VariableFeatures}{Assay}(object, ...) <- value diff --git a/man/VizDimLoadings.Rd b/man/VizDimLoadings.Rd index b71d4a4ea..e8111c48d 100644 --- a/man/VizDimLoadings.Rd +++ b/man/VizDimLoadings.Rd @@ -4,9 +4,17 @@ \alias{VizDimLoadings} \title{Visualize Dimensional Reduction genes} \usage{ -VizDimLoadings(object, dims = 1:5, nfeatures = 30, col = "blue", - reduction = "pca", projected = FALSE, balanced = FALSE, - ncol = NULL, combine = TRUE) +VizDimLoadings( + object, + dims = 1:5, + nfeatures = 30, + col = "blue", + reduction = "pca", + projected = FALSE, + balanced = FALSE, + ncol = NULL, + combine = TRUE +) } \arguments{ \item{object}{Seurat object} diff --git a/man/VlnPlot.Rd b/man/VlnPlot.Rd index b3054f41d..4d221d21b 100644 --- a/man/VlnPlot.Rd +++ b/man/VlnPlot.Rd @@ -4,10 +4,25 @@ \alias{VlnPlot} \title{Single cell violin plot} \usage{ -VlnPlot(object, features, cols = NULL, pt.size = 1, idents = NULL, - sort = FALSE, assay = NULL, group.by = NULL, split.by = NULL, - adjust = 1, y.max = NULL, same.y.lims = FALSE, log = FALSE, - ncol = NULL, combine = TRUE, slot = "data", ...) +VlnPlot( + object, + features, + cols = NULL, + pt.size = 1, + idents = NULL, + sort = FALSE, + assay = NULL, + group.by = NULL, + split.by = NULL, + adjust = 1, + y.max = NULL, + same.y.lims = FALSE, + log = FALSE, + ncol = NULL, + combine = TRUE, + slot = "data", + ... +) } \arguments{ \item{object}{Seurat object} diff --git a/man/WhichCells.Rd b/man/WhichCells.Rd index bd5508239..1ffbde70d 100644 --- a/man/WhichCells.Rd +++ b/man/WhichCells.Rd @@ -8,12 +8,19 @@ \usage{ WhichCells(object, ...) -\method{WhichCells}{Assay}(object, cells = NULL, expression, - invert = FALSE, ...) +\method{WhichCells}{Assay}(object, cells = NULL, expression, invert = FALSE, ...) -\method{WhichCells}{Seurat}(object, cells = NULL, idents = NULL, - expression, slot = "data", invert = FALSE, downsample = Inf, - seed = 1, ...) +\method{WhichCells}{Seurat}( + object, + cells = NULL, + idents = NULL, + expression, + slot = "data", + invert = FALSE, + downsample = Inf, + seed = 1, + ... +) } \arguments{ \item{object}{An object} diff --git a/man/as.Seurat.Rd b/man/as.Seurat.Rd index 1370538e0..247bad39c 100644 --- a/man/as.Seurat.Rd +++ b/man/as.Seurat.Rd @@ -9,16 +9,27 @@ \usage{ as.Seurat(x, ...) -\method{as.Seurat}{CellDataSet}(x, slot = "counts", assay = "RNA", - verbose = TRUE, ...) +\method{as.Seurat}{CellDataSet}(x, slot = "counts", assay = "RNA", verbose = TRUE, ...) -\method{as.Seurat}{loom}(x, cells = "CellID", features = "Gene", - normalized = NULL, scaled = NULL, assay = NULL, verbose = TRUE, - ...) +\method{as.Seurat}{loom}( + x, + cells = "CellID", + features = "Gene", + normalized = NULL, + scaled = NULL, + assay = NULL, + verbose = TRUE, + ... +) -\method{as.Seurat}{SingleCellExperiment}(x, counts = "counts", - data = "logcounts", assay = "RNA", - project = "SingleCellExperiment", ...) +\method{as.Seurat}{SingleCellExperiment}( + x, + counts = "counts", + data = "logcounts", + assay = "RNA", + project = "SingleCellExperiment", + ... +) } \arguments{ \item{x}{An object to convert to class \code{Seurat}} diff --git a/man/as.loom.Rd b/man/as.loom.Rd index 717bab7bd..e4fb73445 100644 --- a/man/as.loom.Rd +++ b/man/as.loom.Rd @@ -7,30 +7,30 @@ \usage{ as.loom(x, ...) -\method{as.loom}{Seurat}(x, assay = NULL, filename = file.path(getwd(), - paste0(Project(object = x), ".loom")), max.size = "400mb", - chunk.dims = NULL, chunk.size = NULL, overwrite = FALSE, - verbose = TRUE, ...) +\method{as.loom}{Seurat}( + x, + assay = NULL, + filename = file.path(getwd(), paste0(Project(object = x), ".loom")), + max.size = "400mb", + chunk.dims = NULL, + chunk.size = NULL, + overwrite = FALSE, + verbose = TRUE, + ... +) } \arguments{ \item{x}{An object to convert to class \code{loom}} -\item{...}{Ignored for now} - \item{assay}{Assay to store in loom file} \item{filename}{The name of the new loom file} -\item{max.size}{Set maximum chunk size in terms of memory usage, unused if \code{chunk.dims} is set; -may pass a character string (eg. \code{3gb}, \code{1200mb}) or exact value in bytes} - -\item{chunk.dims}{Matrix chunk dimensions; auto-determined by default} +\item{chunk.dims}{A one- or two-length integer vector of chunksizes for \code{/matrix}, defaults to 'auto' to automatically determine chunksize} -\item{chunk.size}{Maximum number of cells read/written to disk at once; auto-determined by default} +\item{chunk.size}{How many rows of \code{data} should we stream to the loom file at any given time?} \item{overwrite}{Overwrite an already existing loom file?} - -\item{verbose}{Display a progress bar} } \description{ Convert objects to loom objects diff --git a/man/as.sparse.Rd b/man/as.sparse.Rd index 4b129a335..ec299c8af 100644 --- a/man/as.sparse.Rd +++ b/man/as.sparse.Rd @@ -19,8 +19,13 @@ as.sparse(x, ...) \method{as.sparse}{matrix}(x, ...) -\method{as.data.frame}{Matrix}(x, row.names = NULL, optional = FALSE, - ..., stringsAsFactors = default.stringsAsFactors()) +\method{as.data.frame}{Matrix}( + x, + row.names = NULL, + optional = FALSE, + ..., + stringsAsFactors = default.stringsAsFactors() +) } \arguments{ \item{x}{An object} @@ -32,10 +37,10 @@ as.sparse(x, ...) \item{optional}{logical. If \code{TRUE}, setting row names and converting column names (to syntactic names: see - \code{\link{make.names}}) is optional. Note that all of \R's + \code{\link[base]{make.names}}) is optional. Note that all of \R's \pkg{base} package \code{as.data.frame()} methods use \code{optional} only for column names treatment, basically with the - meaning of \code{\link{data.frame}(*, check.names = !optional)}. + meaning of \code{\link[base]{data.frame}(*, check.names = !optional)}. See also the \code{make.names} argument of the \code{matrix} method.} \item{stringsAsFactors}{logical: should the character vector be converted diff --git a/man/h5ad.Rd b/man/h5ad.Rd index 4b3a980ab..2194fc6f7 100644 --- a/man/h5ad.Rd +++ b/man/h5ad.Rd @@ -12,14 +12,19 @@ ReadH5AD(file, ...) WriteH5AD(object, ...) -\method{ReadH5AD}{character}(file, assay = "RNA", layers = "data", - verbose = TRUE, ...) +\method{ReadH5AD}{character}(file, assay = "RNA", layers = "data", verbose = TRUE, ...) -\method{ReadH5AD}{H5File}(file, assay = "RNA", layers = "data", - verbose = TRUE, ...) +\method{ReadH5AD}{H5File}(file, assay = "RNA", layers = "data", verbose = TRUE, ...) -\method{WriteH5AD}{Seurat}(object, file, assay = NULL, graph = NULL, - verbose = TRUE, overwrite = FALSE, ...) +\method{WriteH5AD}{Seurat}( + object, + file, + assay = NULL, + graph = NULL, + verbose = TRUE, + overwrite = FALSE, + ... +) } \arguments{ \item{file}{Name of h5ad file, or an H5File object for reading in} diff --git a/man/merge.Seurat.Rd b/man/merge.Seurat.Rd index c57d303b1..7c003b9e0 100644 --- a/man/merge.Seurat.Rd +++ b/man/merge.Seurat.Rd @@ -8,11 +8,16 @@ \alias{AddSamples} \title{Merge Seurat Objects} \usage{ -\method{merge}{Assay}(x = NULL, y = NULL, add.cell.ids = NULL, - merge.data = TRUE, ...) +\method{merge}{Assay}(x = NULL, y = NULL, add.cell.ids = NULL, merge.data = TRUE, ...) -\method{merge}{Seurat}(x = NULL, y = NULL, add.cell.ids = NULL, - merge.data = TRUE, project = "SeuratProject", ...) +\method{merge}{Seurat}( + x = NULL, + y = NULL, + add.cell.ids = NULL, + merge.data = TRUE, + project = "SeuratProject", + ... +) } \arguments{ \item{x}{Object} diff --git a/man/print.DimReduc.Rd b/man/print.DimReduc.Rd index 8f622d7f9..7415ef9c3 100644 --- a/man/print.DimReduc.Rd +++ b/man/print.DimReduc.Rd @@ -5,8 +5,7 @@ \alias{print} \title{Print the results of a dimensional reduction analysis} \usage{ -\method{print}{DimReduc}(x, dims = 1:5, nfeatures = 20, - projected = FALSE, ...) +\method{print}{DimReduc}(x, dims = 1:5, nfeatures = 20, projected = FALSE, ...) } \arguments{ \item{x}{An object} diff --git a/man/subset.Seurat.Rd b/man/subset.Seurat.Rd index bbc07badd..403ac8397 100644 --- a/man/subset.Seurat.Rd +++ b/man/subset.Seurat.Rd @@ -8,8 +8,7 @@ \usage{ \method{[}{Seurat}(x, i, j, ...) -\method{subset}{Seurat}(x, subset, cells = NULL, features = NULL, - idents = NULL, ...) +\method{subset}{Seurat}(x, subset, cells = NULL, features = NULL, idents = NULL, ...) } \arguments{ \item{x}{Seurat object to be subsetted} From 9b1cbd84464c0ad1bb85455b3406fc717fbb783f Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Thu, 5 Dec 2019 12:40:14 -0500 Subject: [PATCH 2/8] Update NEWS with additions/changes for v3.1.2 --- NEWS.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/NEWS.md b/NEWS.md index 4936c1d6d..412d35e14 100644 --- a/NEWS.md +++ b/NEWS.md @@ -3,6 +3,17 @@ All notable changes to Seurat will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) +## [3.1.2] - 2019-12-11 +### Added +- New silent slot updater +- New random seed options to `RunCCA`, `RunTSNE`, `WhichCells`, `HTODemux`, `AddModuleScore`, `VlnPlot`, and `RidgePlot` +- Enhancements for dealing with `Assay`-derived objects + +### Changed +- Only run `CalcN` (generates nFeatures and nCounts) when `counts` changes +- Fix issue regarding colons in feature names +- Change object class testing to use `inherits` or `is.*` for R 4.0 compatability + ## [3.1.1] - 2019-09-20 ### Added - New `RegroupIdents` function to reassign idents based on metadata column majority From a195b2287ac2863bf65826f1d57a05bcccb39818 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Thu, 5 Dec 2019 12:41:03 -0500 Subject: [PATCH 3/8] Update README version --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 340161254..0e6576d59 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![CRAN Version](https://www.r-pkg.org/badges/version/Seurat)](https://cran.r-project.org/package=Seurat) [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Seurat)](https://cran.r-project.org/package=Seurat) -# Seurat v3.1.1 +# Seurat v3.1.2 Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC. From 400266a67744c764b24dd48d0c5d3083a02fee33 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Wed, 11 Dec 2019 15:10:30 -0500 Subject: [PATCH 4/8] Update documentation --- NAMESPACE | 2 ++ man/CellsByIdentities.Rd | 27 +++++++++++++++++++++++++++ man/RenameAssays.Rd | 23 +++++++++++++++++++++++ man/RowMergeSparseMatrices.Rd | 2 +- man/as.loom.Rd | 11 +++++++++-- 5 files changed, 62 insertions(+), 3 deletions(-) create mode 100644 man/CellsByIdentities.Rd create mode 100644 man/RenameAssays.Rd diff --git a/NAMESPACE b/NAMESPACE index da934d8f0..b5b51149c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -182,6 +182,7 @@ export(CellCycleScoring) export(CellScatter) export(CellSelector) export(Cells) +export(CellsByIdentities) export(CollapseEmbeddingOutliers) export(CollapseSpeciesExpressionMatrix) export(ColorDimSplit) @@ -273,6 +274,7 @@ export(ReadH5AD) export(Reductions) export(RegroupIdents) export(RelativeCounts) +export(RenameAssays) export(RenameCells) export(RenameIdents) export(ReorderIdent) diff --git a/man/CellsByIdentities.Rd b/man/CellsByIdentities.Rd new file mode 100644 index 000000000..7dc5fa867 --- /dev/null +++ b/man/CellsByIdentities.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/objects.R +\name{CellsByIdentities} +\alias{CellsByIdentities} +\title{Get cell names grouped by identity class} +\usage{ +CellsByIdentities(object, idents = NULL, cells = NULL) +} +\arguments{ +\item{object}{A Seurat object} + +\item{idents}{A vector of identity class levels to limit resulting list to; +defaults to all identity class levels} + +\item{cells}{A vector of cells to grouping to} +} +\value{ +A named list where names are identity classes and values are vectors +of cells beloning to that class +} +\description{ +Get cell names grouped by identity class +} +\examples{ +CellsByIdentities(object = pbmc_small) + +} diff --git a/man/RenameAssays.Rd b/man/RenameAssays.Rd new file mode 100644 index 000000000..17e550096 --- /dev/null +++ b/man/RenameAssays.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/objects.R +\name{RenameAssays} +\alias{RenameAssays} +\title{Rename assays in a \code{Seurat} object} +\usage{ +RenameAssays(object, ...) +} +\arguments{ +\item{object}{A \code{Seurat} object} + +\item{...}{Named arguments as \code{old.assay = new.assay}} +} +\value{ +\code{object} with assays renamed +} +\description{ +Rename assays in a \code{Seurat} object +} +\examples{ +RenameAssays(object = pbmc_small, RNA = 'rna') + +} diff --git a/man/RowMergeSparseMatrices.Rd b/man/RowMergeSparseMatrices.Rd index 3bab2d31f..b1667a0da 100644 --- a/man/RowMergeSparseMatrices.Rd +++ b/man/RowMergeSparseMatrices.Rd @@ -17,7 +17,7 @@ A merged matrix Returns a sparse matrix } \description{ -This function is for use on sparse matrices and +This function is for use on sparse matrices and should not be run on a Seurat object. } \details{ diff --git a/man/as.loom.Rd b/man/as.loom.Rd index e4fb73445..6fe8c7b65 100644 --- a/man/as.loom.Rd +++ b/man/as.loom.Rd @@ -22,15 +22,22 @@ as.loom(x, ...) \arguments{ \item{x}{An object to convert to class \code{loom}} +\item{...}{Ignored for now} + \item{assay}{Assay to store in loom file} \item{filename}{The name of the new loom file} -\item{chunk.dims}{A one- or two-length integer vector of chunksizes for \code{/matrix}, defaults to 'auto' to automatically determine chunksize} +\item{max.size}{Set maximum chunk size in terms of memory usage, unused if \code{chunk.dims} is set; +may pass a character string (eg. \code{3gb}, \code{1200mb}) or exact value in bytes} + +\item{chunk.dims}{Matrix chunk dimensions; auto-determined by default} -\item{chunk.size}{How many rows of \code{data} should we stream to the loom file at any given time?} +\item{chunk.size}{Maximum number of cells read/written to disk at once; auto-determined by default} \item{overwrite}{Overwrite an already existing loom file?} + +\item{verbose}{Display a progress bar} } \description{ Convert objects to loom objects From ce52f9cf404958c1a26df4ff6a5c47ded2f2a445 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Wed, 11 Dec 2019 16:47:42 -0500 Subject: [PATCH 5/8] Add biocViews to DESCRIPTION to facilitate installation of bioc dependencies --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index f508a03a2..1f8ad0e6d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -83,6 +83,7 @@ Collate: 'zzz.R' RoxygenNote: 7.0.2 Encoding: UTF-8 +biocViews: Suggests: loomR, testthat, From 10eca2226f682bf107f9a2c0fcdd387f80c0dcff Mon Sep 17 00:00:00 2001 From: Andrew Butler Date: Thu, 12 Dec 2019 09:37:47 -0500 Subject: [PATCH 6/8] fix CellCycleScoring to work with new names fix --- R/utilities.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/utilities.R b/R/utilities.R index a52977b2e..e37123559 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -432,7 +432,7 @@ CellCycleScoring <- function( set.ident = FALSE, ... ) { - name <- 'Cell Cycle' + name <- 'Cell.Cycle' features <- list('S.Score' = s.features, 'G2M.Score' = g2m.features) object.cc <- AddModuleScore( object = object, From 933eca00cf2543a867017cb2670403bf41a7cae1 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Thu, 12 Dec 2019 12:30:38 -0500 Subject: [PATCH 7/8] Require UWOT v0.1.5 or higher See satijalab/seurat#2256 for more details --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1f8ad0e6d..c7a4b4e5d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -62,7 +62,7 @@ Imports: tools, tsne, utils, - uwot + uwot (>= 0.1.5) LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress License: GPL-3 | file LICENSE LazyData: true From 04ebc61b5ff7f5ddf5b75c76b6c7155daace94da Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Thu, 12 Dec 2019 16:06:57 -0500 Subject: [PATCH 8/8] Update cran-comments --- cran-comments.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index e81ae694b..1023d2cba 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,11 +1,11 @@ -# Seurat v3.1.1 +# Seurat v3.1.2 ## Test environments -* local Ubuntu 16.04.6 and 18.04.2 installs, R 3.5.3 +* local Ubuntu 16.04.6 and 18.04.2 installs, R 3.6.1 * Ubuntu 16.04.6 (on travis-ci), R 3.6.1 * macOS 10.13.3 (on travis-ci), R 3.6.1 * Windows Server 2012 R2 (on AppVeyor), R 3.6.1 Patched -* win-builder (oldrelease, release, devel) +* win-builder (oldrelease, release, devel, devel_gcc8) ## R CMD check results There were no ERRORs or WARNINGs @@ -33,4 +33,6 @@ There were 3 NOTEs: ## Downstream dependencies -There are three packages that suggest Seurat: BisqueRNA, clustreen, and iCellR; this update does not impact their functionality. +There is one pacakge that imports Seurat: multicross; this update does not impact its functionality + +There are five packages that suggest Seurat: BisqueRNA, clustree, diem, iCellR, and Rmagic; this update does not impact their functionality.