From 223d638f5aa5017c4a934d6613cb2c879341334f Mon Sep 17 00:00:00 2001 From: vertesy Date: Fri, 20 Sep 2024 00:58:58 +0200 Subject: [PATCH] ... --- R/Seurat.Utils.Visualization.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/R/Seurat.Utils.Visualization.R b/R/Seurat.Utils.Visualization.R index 487f72b..070c72c 100644 --- a/R/Seurat.Utils.Visualization.R +++ b/R/Seurat.Utils.Visualization.R @@ -2035,6 +2035,7 @@ qSeuViolin <- function( obj@meta.data[[feature]] <- na.replace(x = obj@meta.data[[feature]], replace = 0) } + # browser() if (clip.outliers) { warning("Outliers are clipped at percentiles 0.5% and 99.5%", immediate. = TRUE) obj@meta.data[[feature]] <- CodeAndRoll2::clip.outliers.at.percentile( @@ -3297,14 +3298,14 @@ scEnhancedVolcano <- function( # Clip p-values. toptable[["p_val_adj"]] <- - clip.at.fixed.value(distribution = toptable[["p_val_adj"]], thr = min.p, high = F) + clip.at.fixed.value(x = toptable[["p_val_adj"]], thr = min.p, high = F) # Clip log2FC. if (max.l2fc < Inf) { toptable[["avg_log2FC"]] <- - clip.at.fixed.value(distribution = toptable[["avg_log2FC"]], thr = -max.l2fc, high = F) + clip.at.fixed.value(x = toptable[["avg_log2FC"]], thr = -max.l2fc, high = F) toptable[["avg_log2FC"]] <- - clip.at.fixed.value(distribution = toptable[["avg_log2FC"]], thr = max.l2fc, high = T) + clip.at.fixed.value(x = toptable[["avg_log2FC"]], thr = max.l2fc, high = T) } # Add statistical information to the subtitle.