Sync with NIDAP Global code, 2024-05-31

NIDAP-Community · Jun 3, 2024 · e3bcb53 · e3bcb53
1 parent 7cba94e
commit e3bcb53
Showing 1 changed file with 12 additions and 12 deletions.
diff --git a/R/Filter_Seurat_Object_by_Metadata.R b/R/Filter_Seurat_Object_by_Metadata.R
@@ -137,9 +137,6 @@ filterSeuratObjectByMetadata <- function(object,
   ## --------------- ##
 
 
-
-
-
   ## --------------- ##
   ## Functions       ##
   ## --------------- ##
@@ -216,7 +213,7 @@ filterSeuratObjectByMetadata <- function(object,
       xlab("umap-1") + ylab("umap-2")
     return(plot2)
   }
-
+  
   .distinctColorPalette <- function(k = 1, seed) {
     current.color.space <- our.color.space@coords
     # Set iter.max to 20 to avoid convergence warnings.
@@ -264,12 +261,12 @@ filterSeuratObjectByMetadata <- function(object,
 
   ## Get colors from user parameter and add more if the default list is too short.
   if (class(object@meta.data[[category.to.filter[1]]]) != "numeric") {
-    col.length = length(levels(as.factor(Filter.orig[colname])))
+    col.length = length(levels(as.factor(Filter.orig)))
     if (length(colors) < col.length) {
       more.cols = .distinctColorPalette(col.length - length(colors), 10)
       colors <- c(colors, more.cols)
     }
-    names(colors) <- levels(as.factor(Filter.orig[colname]))
+    names(colors) <- levels(as.factor(Filter.orig))
 
     ## Keep or remove cells based on user input values.
     if (keep.or.remove) {
@@ -316,14 +313,16 @@ filterSeuratObjectByMetadata <- function(object,
     ## Make before and after plots.
     title <-
       paste0("filtered by ",
-             category.to.filter[1],
-             " and split by ",
-             category.to.filter[2])
+             category.to.filter[1]#,
+             ##             " and split by ",
+             ##             category.to.filter[2]
+      )
     plot1 = DimPlot(
       object,
       reduction = reduction,
       group.by = colname,
-      pt.size = dot.size
+      pt.size = dot.size,
+      raster=FALSE
     ) +
       theme_classic() +
       scale_color_manual(values = colors) +
@@ -338,7 +337,8 @@ filterSeuratObjectByMetadata <- function(object,
       reduction = reduction,
       cells.highlight = idx,
       cols.highlight = rev(cols2[1:filt.length]),
-      sizes.highlight = dot.size.highlighted.cells
+      sizes.highlight = dot.size.highlighted.cells,
+      raster=FALSE
     ) +
       theme_classic() +
       theme(legend.position = legend.position) +
@@ -389,7 +389,7 @@ filterSeuratObjectByMetadata <- function(object,
 
   }
 
-
+  
 
   result.list <- list("object" = SO.sub,
                       "plot1" = plot1,