diff --git a/R/Seurat.Utils.R b/R/Seurat.Utils.R index dd7eda0..21b2272 100644 --- a/R/Seurat.Utils.R +++ b/R/Seurat.Utils.R @@ -3535,9 +3535,9 @@ xsave <- function( try(obj@misc$all.genes <- all.genes, silent = TRUE) } - fnameBase <- trimws(kppu(prefix, substitute(obj), suffix, project, preset, "compr", idate(Format = "%Y.%m.%d_%H.%M")), whitespace = "_") + fnameBase <- trimws(kppu(prefix, substitute(obj), suffix, project, idate(Format = "%Y.%m.%d_%H.%M")), whitespace = "_") # , preset, "compr" FNN <- paste0(out_dir, fnameBase, ".qs") - iprint(substitute(obj), '<- xread("', FNN, '")') + print(paste0(substitute(obj), " <- xread('", FNN, "')" )) if (background_job & rstudioapi::isAvailable()) { "This part is not debugged yet!" diff --git a/R/Seurat.Utils.Visualization.R b/R/Seurat.Utils.Visualization.R index e60a68b..baa3692 100644 --- a/R/Seurat.Utils.Visualization.R +++ b/R/Seurat.Utils.Visualization.R @@ -723,11 +723,17 @@ qFeatureScatter <- function( #' #' @export qSeuViolin <- function( - object = ls.Seurat[[1]], suffix = GEX_library, - features = "nFeature_RNA", split.by = "orig.ident", logY = TRUE, hline = FALSE, caption = FALSE - , ...) { + object = ls.Seurat[[1]], + split.by, + idents = GetNamedClusteringRuns(object)[1], + suffix = GEX_library, + features = "nFeature_RNA", + logY = TRUE, hline = FALSE, caption = FALSE, + ...) { + + print(unique(idents)) - p <- VlnPlot(object = object, features = features, split.by = split.by, ...) + + p <- VlnPlot(object = object, features = features, split.by = split.by, group.by = idents, ...) + ggtitle(label = features, subtitle = paste(suffix, "by", split.by)) + theme(axis.title.x = element_blank()) + labs(y = "Top UVI's depth")