Merge pull request #12 from jiajic/dev

Add sankey plotting

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GiottoVisuals
-Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9003
+Title: Visuals for the Giotto spatial biology analysis ecosystem
+Version: 0.0.0.9004
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre")),
@@ -84,6 +84,7 @@ Collate:
     'globals.R'
     'plot_dendrogram.R'
     'plot_heatmap.R'
+    'plot_sankey.R'
     'plot_scatter.R'
     'plot_violin.R'
     'spatialDE_visuals.R'

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export("sankeyLabel<-")
 export(FSV_show)
 export(addGiottoImageToSpatPlot)
 export(colorRamp2)
@@ -16,6 +17,7 @@ export(getColors)
 export(getDistinctColors)
 export(get_continuous_colors)
 export(gg_simple_scatter)
+export(giottoSankeyPlan)
 export(pal_names)
 export(plotHeatmap)
 export(plotMetaDataCellsHeatmap)
@@ -31,6 +33,9 @@ export(plotUMAP)
 export(plotUMAP_2D)
 export(plotUMAP_3D)
 export(plot_output_handler)
+export(sankeyLabel)
+export(sankeySet)
+export(sankeySetAddresses)
 export(set_default_color_continuous)
 export(set_default_color_continuous_CCcom_dotplot)
 export(set_default_color_continuous_CCcom_heatmap)
@@ -70,7 +75,13 @@ export(spatNetwDistributionsKneighbors)
 export(spatPlot)
 export(spatPlot2D)
 export(spatPlot3D)
+export(subsetSankeySet)
 export(violinPlot)
+exportClasses(giottoSankeyPlan)
+exportMethods("+")
+exportMethods("sankeyRelate<-")
+exportMethods(sankeyPlot)
+exportMethods(sankeyRelate)
 import(GiottoClass)
 import(GiottoUtils)
 import(ggplot2)
@@ -79,6 +90,8 @@ importClassesFrom(data.table,data.table)
 importFrom(colorRamp2,colorRamp2)
 importFrom(data.table,dcast)
 importFrom(data.table,dcast.data.table)
+importFrom(methods,setGeneric)
+importFrom(methods,setMethod)
 importFrom(methods,slot)
 importFrom(stats,cov)
 importFrom(stats,var)

R/dd.R

@@ -203,3 +203,9 @@ NULL
 
 
 
+# Documentation dummy for methods that are defined elsewhere
+#' @title hidden_aliases
+#' @name hidden_aliases
+NULL
+
+

R/package_imports.R

@@ -3,6 +3,7 @@
 #' @importFrom data.table dcast dcast.data.table
 #' @importFrom stats cov var
 #' @importFrom methods slot
+#' @importFrom methods setGeneric setMethod
 #' @importFrom colorRamp2 colorRamp2
 #' @import GiottoUtils
 #' @import GiottoClass