...

Development/Create_the_Seurat.utils_Package.R

@@ -1,7 +1,7 @@
 ######################################################################################################
 # Create_the_Seurat.utils_Package.R
 ######################################################################################################
-# source("/Users/abel.vertesy/GitHub/Packages/Seurat.utils/Development/Create_the_Seurat.utils_Package.v0.1.R")
+# source("~/GitHub/Packages/Seurat.utils/Development/Create_the_Seurat.utils_Package.v0.1.R")
 # rm(list = ls(all.names = TRUE));
 try(dev.off(), silent = TRUE)
 
@@ -58,6 +58,7 @@ if ( !dir.exists(RepositoryDir) ) { create(path = RepositoryDir, description = D
 }
 
 
+
 # go and write fun's ------------------------------------------------------------------------
 # file.edit(Package_FnP)
 

R/Seurat.Utils.R

@@ -1195,7 +1195,7 @@ recall.parameters <- function(obj = combined.obj, overwrite = FALSE) {
   obj <- ww.get.1st.Seur.element(obj)
 
   if ('p' %in% names(obj@misc)) {
-    if (!exists('p')) iprint("variable 'p' exits in the global namespace:", head(p))
+    if (exists('p')) iprint("variable 'p' exits in the global namespace:", head(p))
 
     if (!exists('p') | (exists('p') & overwrite == TRUE) ) {
       MarkdownHelpers::ww.assign_to_global(name = "p", value = obj@misc$'p'); print("Overwritten.")
@@ -3048,6 +3048,7 @@ multiFeaturePlot.A4 <- function(list.of.genes # Save multiple FeaturePlots, as j
                                 , saveGeneList = FALSE
                                 , w = wA4, h = hA4, scaling = 1
                                 , format = c('jpg', 'pdf', 'png')[1]
+                                # , solo = MarkdownHelpers::FALSE.unless('b.plot.solo')
                                 , raster = MarkdownHelpers::FALSE.unless('b.raster')
                                 , raster.dpi = c(512, 512)/4
                                 , ...

R/Test.R

@@ -0,0 +1,84 @@
+
+
+plot.qUMAPs.in.a.folder <- function(genes, obj = combined.obj, foldername = NULL, intersectionAssay = 'RNA', plot.reduction = 'umap', ...) {
+
+  ParentDir = OutDir
+  if (is.null(foldername)) foldername = substitute(genes)
+  create_set_SubDir( paste0(foldername,'-', plot.reduction),'/')
+  list.of.genes.found = check.genes(list.of.genes = genes, obj = obj, assay.slot = intersectionAssay, makeuppercase = F)
+
+
+  for (g in list.of.genes.found) {
+    qUMAP(g, reduction = plot.reduction, ...)
+  }
+  MarkdownReports::create_set_OutDir(... = ParentDir)
+}
+
+
+
+multiFeaturePlot.A4 <- function(list.of.genes # Save multiple FeaturePlots, as jpeg, on A4 for each gene, which are stored as a list of gene names.
+                                , obj = combined.obj
+                                , foldername = substitute(list.of.genes), plot.reduction='umap'
+                                , intersectionAssay = c('RNA', 'integrated')[1]
+                                , layout = c('tall', 'wide', FALSE )[2]
+                                , colors = c("grey", "red"), nr.Col = 2, nr.Row =4, cex = round(0.1/(nr.Col*nr.Row), digits = 2)
+                                , gene.min.exp = 'q01', gene.max.exp = 'q99', subdir =T
+                                , prefix = NULL , suffix = NULL
+                                , background_col = "white"
+                                , aspect.ratio = c(FALSE, 0.6)[2]
+                                , saveGeneList = FALSE
+                                , w = wA4, h = hA4, scaling = 1
+                                , format = c('jpg', 'pdf', 'png')[1]
+                                , solo = MarkdownHelpers::FALSE.unless('b.solo.plot')
+                                , raster = MarkdownHelpers::FALSE.unless('b.raster')
+                                , raster.dpi = c(512, 512)/4
+                                , ...
+                                # , jpeg.res = 225, jpeg.q = 90
+) {
+  tictoc::tic()
+  ParentDir = OutDir
+  if (is.null(foldername)) foldername = "genes"
+  if (subdir) create_set_SubDir( paste0(foldername,'-', plot.reduction),'/')
+  list.of.genes.found = check.genes(list.of.genes = list.of.genes, obj = obj, assay.slot = intersectionAssay, makeuppercase = F)
+  DefaultAssay(obj) <- intersectionAssay
+
+  if (layout == 'tall') { w = wA4 * scaling; h = hA4 * scaling; nr.Col = 2; nr.Row = 4; print('layout active, nr.Col ignored.') }
+  if (layout == 'wide') { w = hA4 * scaling; h = wA4 * scaling; nr.Col = 2; nr.Row = 2; print('layout active, nr.Col ignored.') }
+
+  lsG = iterBy.over(1:length(list.of.genes.found), by = nr.Row * nr.Col)
+  for (i in 1:length(lsG)) {
+    genes = list.of.genes.found[lsG[[i]]]
+    iprint(i,genes )
+    plotname = kpp(c(prefix, plot.reduction,i, genes, suffix, format ))
+
+    if (solo) {
+
+
+    } else {
+      plot.list = Seurat::FeaturePlot(object = obj, features = genes, reduction = plot.reduction, combine = F
+                                      , ncol = nr.Col, cols = colors
+                                      , min.cutoff = gene.min.exp, max.cutoff = gene.max.exp
+                                      , raster = TRUE, raster.dpi = raster.dpi
+                                      , pt.size = cex, ...)
+
+      for (i in 1:length(plot.list)) {
+        plot.list[[i]] <- plot.list[[i]] + NoLegend() + NoAxes()
+        if (aspect.ratio) plot.list[[i]] <- plot.list[[i]] + ggplot2::coord_fixed(ratio = aspect.ratio)
+      }
+
+      pltGrid <- cowplot::plot_grid(plotlist = plot.list, ncol = nr.Col, nrow = nr.Row )
+      ggsave(filename = plotname, width = w, height = h, bg = background_col, plot = pltGrid)
+    }
+  }
+
+
+  if (subdir) MarkdownReports::create_set_OutDir(... = ParentDir)
+  if (saveGeneList) {
+    if (is.null(obj@misc$gene.lists)) obj@misc$gene.lists <- list()
+    obj@misc$gene.lists[[substitute(list.of.genes)]] <- list.of.genes.found
+    print("Genes saved under: obj@misc$gene.lists")
+    return(obj)
+  }
+  tictoc::toc()
+};
+

Seurat.utils.Rproj

@@ -5,8 +5,13 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
 Encoding: UTF-8
 
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 LineEndingConversion: Posix