Change column for plotting positives and negatives from adjP to rawP

waldronlab · Sep 12, 2024 · 238805f · 238805f
1 parent f223985
commit 238805f
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/vignettes/articles/HMP_2012_16S_gingival_V13.Rmd b/vignettes/articles/HMP_2012_16S_gingival_V13.Rmd
@@ -241,7 +241,7 @@ positives <- createPositives(
     object = DA_output,
     priorKnowledge = prior_info, 
     enrichmentCol = "taxon_annotation", namesCol = "new_names",
-    slot = "pValMat", colName = "adjP", type = "pvalue",
+    slot = "pValMat", colName = "rawP", type = "pvalue",
     # direction = direction,
     direction = direction,
     threshold_pvalue = 1,

diff --git a/vignettes/articles/Ravel_2011_16S_BV.Rmd b/vignettes/articles/Ravel_2011_16S_BV.Rmd
@@ -218,7 +218,7 @@ positives <- createPositives(
     object = DA_output, 
     priorKnowledge = prior_info, 
     enrichmentCol = "taxon_annotation", namesCol = "taxon_name",
-    slot = "pValMat", colName = "adjP", type = "pvalue",
+    slot = "pValMat", colName = "rawP", type = "pvalue",
     direction = direction,
     threshold_pvalue = 1,
     threshold_logfc = 0,