1. GeneTonic
  2. Commit 40ea0944fb6599c70ba329cd7ed8c240474b0bfb
Browse code

specifying to omit the NA from the ranges calculations

Federico Marini authored on 07/10/2022 11:42:32
Showing 2 changed files
R/enrichment_map.R
History View file @ 40ea094
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@@ -177,7 +177,7 @@ enrichment_map <- function(res_enrich,
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     V(emg)$color.hover <- map2color(col_var, mypal_hover, symmetric = FALSE, limits = range(col_var))
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   } else {
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     # e.g. using z_score or aggregated value
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-    if (prod(range(col_var)) >= 0) {
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+    if (prod(range(na.omit(col_var))) >= 0) {
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       # gradient palette
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       mypal <- (scales::alpha(
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         colorRampPalette(RColorBrewer::brewer.pal(name = "Oranges", 9))(50), 0.8
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@@ -190,9 +190,12 @@ enrichment_map <- function(res_enrich,
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       ))
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       # V(g)$color <- map2color(colVar,mypal,limits = range(colVar))
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-      V(emg)$color.background <- map2color(col_var, mypal, symmetric = FALSE, limits = range(col_var))
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-      V(emg)$color.highlight <- map2color(col_var, mypal_select, symmetric = FALSE, limits = range(col_var))
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-      V(emg)$color.hover <- map2color(col_var, mypal_hover, symmetric = FALSE, limits = range(col_var))
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+      V(emg)$color.background <- map2color(col_var, mypal, symmetric = FALSE,
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+                                           limits = range(na.omit(col_var)))
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+      V(emg)$color.highlight <- map2color(col_var, mypal_select, symmetric = FALSE,
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+                                          limits = range(na.omit(col_var)))
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+      V(emg)$color.hover <- map2color(col_var, mypal_hover, symmetric = FALSE,
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+                                      limits = range(na.omit(col_var)))
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     } else {
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       # divergent palette to be used
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       mypal <- rev(scales::alpha(
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@@ -206,9 +209,12 @@ enrichment_map <- function(res_enrich,
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       ))
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       # V(g)$color <- map2color(colVar,mypal,limits = range(colVar))
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-      V(emg)$color.background <- map2color(col_var, mypal, symmetric = TRUE, limits = range(col_var))
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-      V(emg)$color.highlight <- map2color(col_var, mypal_select, symmetric = TRUE, limits = range(col_var))
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-      V(emg)$color.hover <- map2color(col_var, mypal_hover, symmetric = TRUE, limits = range(col_var))
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+      V(emg)$color.background <- map2color(col_var, mypal, symmetric = TRUE,
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+                                           limits = range(na.omit(col_var)))
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+      V(emg)$color.highlight <- map2color(col_var, mypal_select, symmetric = TRUE,
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+                                          limits = range(na.omit(col_var)))
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+      V(emg)$color.hover <- map2color(col_var, mypal_hover, symmetric = TRUE,
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+                                      limits = range(na.omit(col_var)))
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     }
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   }
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R/gs_dendro.R
History View file @ 40ea094
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@@ -152,7 +152,7 @@ gs_dendro <- function(res_enrich,
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     } else {
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       # e.g. using z_score or aggregated value
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-      if (prod(range(col_var)) >= 0) {
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+      if (prod(range(na.omit(col_var))) >= 0) {
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         # gradient palette
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         mypal <- (scales::alpha(
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           colorRampPalette(RColorBrewer::brewer.pal(name = "Oranges", 9))(50), 0.8