From 89a747748e069cdb13600923afee45d8fcf52b9a Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Mon, 26 Feb 2024 12:47:23 -0500 Subject: [PATCH] figure legend updates after adding more panels --- content/100.figure-table-legends.md | 29 +++++++++++++++++------------ 1 file changed, 17 insertions(+), 12 deletions(-) diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index 50d62d7..76be6f4 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -17,16 +17,21 @@ Where available, submitter-provided citation information as well as other databa **Figure 2. Overview of ScPCA Portal workflow.** A. Primary workflow for processing single-cell and single-nuclei data for the ScPCA Portal. -Mapping is first performed with `alevin-fry` to generate a gene-by-cell count matrix. -This matrix is read into R and converted into a `SingleCellExperiment` (`SCE`) object. -This `SCE` object is exported as the `Unfiltered SCE Object` without any additional processing. -First, empty droplets are filtered out, and the resulting `SCE` is exported as the `Filtered SCE Object`. -Next, the filtered object undergoes additional post-processing, including filtering out low-quality cells, normalizing counts, and performing dimension reduction (principle components and UMAP embeddings). -Finally, the object undergoes cell type annotation and is exported as the `Processed SCE Object`. -A summary QC report as well as a supplemental cell type report are prepared and exported. -All `SCE` files are converted to `AnnData` format and exported. -B. Representative figures that appear in the summary QC report. -Top row from left to right: The total UMI count for each droplet against the droplet's rank, where points are colored by the percentage of droplets that pass the cell filter used to create the `Filtered SCE Object`; Number of genes detected for each cell passing the cell filter again the total UMI count, where points are colored by the percentage of mitochondrial reads in the cell; `miQC` model diagnostic plot showing the percent of mitochondrial reads in each cell against the number of genes detected in the `Filtered SCE Object`, where points are colored by the probability that the cell is compromised as determined by `miQC`. -The `miQC` model diagnostic plot is only present for libraries that were filtered with `miQC`. -Bottom row from left to right: The percent of mitochondrial reads in each cell, as determined either by `miQC` or by a minimum unique gene count cutoff, against the number of genes detected in each cell, where points are colored by whether the cell was kept or removed prior to normalization and dimensionality reduction; UMAP embeddings where each cell is colored by the number of genes detected; UMAP embeddings for the top four most variable genes where each cell is colored by the log-normalized gene expression. +Mapping is first performed with `alevin-fry` to generate a gene-by-cell count matrix, which is read into `R` and converted into a `SingleCellExperiment` (`SCE`) object. +This `SCE` object is exported as the `Unfiltered SCE Object` before further post-processing. +Next, empty droplets are filtered out, and the resulting `SCE` is exported as the `Filtered SCE Object`. +The filtered object undergoes additional post-processing, including filtering out low-quality cells, normalizing counts, and performing dimension reduction including principal components analysis and UMAP calculation. +The object undergoes cell type annotation and is exported as the `Processed SCE Object`. +A summary QC report and a supplemental cell type report are prepared and exported. +Finally, all `SCE` files are converted to `AnnData` format and exported. + +Panels B-G show example figures that appear in the summary QC report, shown here for `SCPCL000001`, as follows. +B. The total UMI count for each droplet against the droplet's rank, where points are colored by the percentage of droplets that pass the cell filter used to create the `Filtered SCE Object`. +C. The number of genes detected for each cell passing the cell filter again the total UMI count, where points are colored by the percentage of mitochondrial reads in the cell. +D. `miQC` model diagnostic plot showing the percent of mitochondrial reads in each cell against the number of genes detected in the `Filtered SCE Object`, where points are colored by the probability that the cell is compromised as determined by `miQC`. +The `miQC` model diagnostic plot is only present in summary QC reports whose libraries that were filtered with `miQC`. +E. The percent of mitochondrial reads in each cell, as determined either by `miQC` or by a minimum unique gene count cutoff, against the number of genes detected in each cell. +Points are colored by whether the cell was kept or removed prior to normalization and dimensionality reduction. +F. UMAP embeddings of log-normalized RNA expression values where each cell is colored by the number of genes detected. +G. UMAP embeddings of log-normalized RNA expression values for the top four most variable genes where each cell is colored by the given gene's expression. In the actual summary QC report, the top 12 most highly variable genes are shown.