Merge pull request satijalab#876 from satijalab/ig_marker_sorting

Updated marker sorting
zm19911213 · Nov 10, 2023 · b6217b1 · b6217b1
2 parents 79c2bec + 2ddf7f4
commit b6217b1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 5.0.0.9002
-Date: 2023-11-10
+Version: 5.0.0.9003
+Date: 2023-10-23
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(

diff --git a/R/differential_expression.R b/R/differential_expression.R
@@ -164,7 +164,7 @@ FindAllMarkers <- function(
           subset = (myAUC > return.thresh | myAUC < (1 - return.thresh))
         )
       } else if (is.null(x = node) || test.use %in% c('bimod', 't')) {
-        gde <- gde[order(gde$p_val, -gde[, 2]), ]
+        gde <- gde[order(gde$p_val, -abs(gde$pct.1-gde$pct.2)), ]
         gde <- subset(x = gde, subset = p_val < return.thresh)
       }
       if (nrow(x = gde) > 0) {
@@ -612,7 +612,7 @@ FindMarkers.default <- function(
   if (test.use %in% DEmethods_nocorrect()) {
     de.results <- de.results[order(-de.results$power, -de.results[, 1]), ]
   } else {
-    de.results <- de.results[order(de.results$p_val, -abs(de.results[,colnames(fc.results)[1]])), ]
+    de.results <- de.results[order(de.results$p_val, -abs(de.results$pct.1-de.results$pct.2)), ]
     de.results$p_val_adj = p.adjust(
       p = de.results$p_val,
       method = "bonferroni",