include groups in lefserPlot, refers to #15

waldronlab · Sep 6, 2023 · e2b90fd · e2b90fd
1 parent 8114c16
commit e2b90fd
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Showing 2 changed files with 14 additions and 2 deletions.
diff --git a/R/lefser.R b/R/lefser.R
@@ -264,6 +264,7 @@ lefser <-
     }
     group <- .numeric01(groupf)
     groups <- 0:1
+    names(groups) <- groupsf
     expr_data <- assay(expr, i = assay)
     expr_sub <- filterKruskal(expr = expr_data, group = group, p.value = kruskal.threshold)
 
@@ -315,5 +316,8 @@ lefser <-
     scores_df <- .trunc(scores_df, trim.names)
 
     threshold_scores <- abs(scores_df$scores) >= lda.threshold
-    scores_df[threshold_scores, ]
+    res_scores <- scores_df[threshold_scores, ]
+    class(res_scores) <- c("lefser_df", class(res_scores))
+    attr(res_scores, "groups") <- groups
+    res_scores
   }
diff --git a/R/lefserPlot.R b/R/lefserPlot.R
@@ -28,7 +28,15 @@ utils::globalVariables(c("Names", "scores"))
 lefserPlot <- function(df, colors = c("red", "forestgreen"), 
                        trim.names = TRUE) {
   df <- .trunc(df, trim.names)
-  group <- ifelse(df$scores > 0, 1, 0)
+  groups <- attr(df, "groups")
+  if (is.null(groups))
+      group <- ifelse(df$scores > 0, 1, 0)
+  else
+      group <- ifelse(
+          df$scores > 0,
+          names(groups)[groups == 1],
+          names(groups)[groups == 0]
+      )
   df$group <- as.factor(group)
   plt <-
     ggplot(df, aes(reorder(Names, scores), scores)) + ylab("LDA SCORE (log 10)") +