feat: change default behavior of visualize_markers

scripts/export.R

@@ -405,6 +405,8 @@ visualize_markers <- function(
     height = 8,
     ...
 ){
+  # catch extra arguments
+  extra_args <- list(...)
   # define colormap
   cmap <- get(colormap, envir = loadNamespace("pals"))
   cols <- unname(cmap(nlevels(object@active.ident)))
@@ -418,34 +420,52 @@ visualize_markers <- function(
   ifelse(!dir.exists(file.path(savedir, subdir)),
          dir.create(file.path(savedir, subdir), recursive=TRUE),
          FALSE)
-
   # save the violin plot
-  filepath <- file.path(savedir, subdir, prefix)
-  gg <- suppressMessages(
-    VlnPlot(object, features = features, pt.size = 0, cols = cols)
+  for (feat in features){
+    filepath <- file.path(savedir, subdir, feat)
+    vln_args <- c(
+      list("object" = object, "features" = feat, "pt.size" = 0, "cols" = cols),
+      extra_args[names(extra_args) %in% names(as.list(args(VlnPlot)))]
     )
+    gg <- suppressMessages(do.call(VlnPlot, vln_args))
     ggsave(file=paste0(filepath, "_vlnplot", ".", device), device = device,
-         width = width, height = width, gg, ...)
-
+           width = width, height = width, gg)
+  }
   # save the feature plot with custom gradient
+  max_cmap <- SeuratObject::FetchData(
+    object = object,
+    vars = features,
+    slot = "data"
+  ) %>% max()
+  for (feat in features){
+    filepath <- file.path(savedir, subdir, feat)
+    feat_args <- c(
+      list("object" = object, "features" = feat),
+      extra_args[names(extra_args) %in% names(as.list(args(FeaturePlot)))]
+    )
     gg <- suppressMessages(
-    FeaturePlot(object, features = features) & 
+      do.call(FeaturePlot, feat_args) & 
         scale_color_gradientn(
-            colors = cmap_vir, limits = c(na_cutoff, NA), na.value = na_color)
+          colors = cmap_vir, limits = c(na_cutoff, max_cmap), na.value = na_color)
     )
     ggsave(file=paste0(filepath, "_featplot", ".", device), device = device,
-         width = width, height = height, gg, ...)
-
+           width = width, height = height, gg)
+  }
   # save the dot plot with custom gradient
+  filepath <- file.path(savedir, subdir, prefix)
+  dot_args <- c(
+    list("object" = object, "features" = features),
+    extra_args[names(extra_args) %in% names(as.list(args(DotPlot)))]
+  )
   gg <- suppressWarnings(suppressMessages(
-    DotPlot(object, features = features) & 
+    do.call(DotPlot, dot_args) &
       theme_custom() &
       scale_x_discrete(guide = guide_axis(n.dodge = 2)) & 
           scale_color_gradientn(
             colors = cmap_vir, limits = c(na_cutoff, NA), na.value = na_color)
   ))
   ggsave(file=paste0(filepath, "_dotplot", ".", device), device = device,
-         width = width, height = height, gg, ...)
+         width = width, height = height, gg)
 
   return(NULL)
 }