changed figure details

saezlab · Jun 28, 2024 · 61b55d7 · 61b55d7
1 parent 5a01a77
commit 61b55d7
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Showing 2 changed files with 16 additions and 6 deletions.
diff --git a/workflow/scripts/05_figures_manuscript/01_figure_overview_priors.R b/workflow/scripts/05_figures_manuscript/01_figure_overview_priors.R
@@ -164,7 +164,7 @@ kin_list <- map(prior, function(df){
 })
 kin_comb <- make_comb_mat(kin_list)
 
-pdf(upset_kin, width = 6, height = 3)
+pdf(upset_kin, width = 5, height = 3)
 UpSet(kin_comb, pt_size = unit(2, "mm"), lwd = 1)
 dev.off()
 
@@ -173,7 +173,7 @@ edge_list <- map(prior, function(df){
 })
 edge_comb <- make_comb_mat(edge_list)
 
-pdf(upset_edge, width = 6, height = 3)
+pdf(upset_edge, width = 5.5, height = 3)
 UpSet(edge_comb, pt_size = unit(2, "mm"), lwd = 1)
 dev.off()
 
@@ -279,7 +279,7 @@ kintype_p <- ggplot(kin_type, aes(x = resource, y = n, fill = kinase)) +
         text = element_text(size = 10),
         legend.key.size = unit(0.2, 'cm'))
 
-pdf(kintype_pdf, height = 3, width = 4.5)
+pdf(kintype_pdf, height = 3, width = 4.2)
 kintype_p
 dev.off()
 
@@ -303,7 +303,7 @@ regulonsize_p <- ggplot(set_size, aes(x = prior, y = n_targets)) +
         text = element_text(size = 10),
         legend.key.size = unit(0.2, 'cm'))
 
-pdf(regulonsize_pdf, height = 3, width = 3)
+pdf(regulonsize_pdf, height = 3, width = 2.8)
 regulonsize_p
 dev.off()
 
diff --git a/workflow/scripts/05_figures_manuscript/03_figure_benchmark.R b/workflow/scripts/05_figures_manuscript/03_figure_benchmark.R
@@ -138,7 +138,12 @@ med_mat <- bench_df %>%
   column_to_rownames("net")
 med_mat
 
-col_fun = colorRamp2(c(min(med_mat, na.rm = T), max(med_mat, na.rm = T)), c("white", "deeppink4"))
+col_fun = colorRamp2(
+  c(min(med_mat, na.rm = TRUE), mean(unlist(as.vector(med_mat)), na.rm = TRUE), max(med_mat, na.rm = TRUE)),
+  c("white", "#edcac6", "#7F0863")
+)
+
+#col_fun = colorRamp2(c(min(med_mat, na.rm = T), max(med_mat, na.rm = T)), c("white", "deeppink4"))
 column_ha = HeatmapAnnotation(mean_method = colMeans(med_mat, na.rm = T), col = list(mean_method = col_fun))
 row_ha = rowAnnotation(mean_prior = rowMeans(med_mat, na.rm = T), col = list(mean_prior = col_fun))
 
@@ -183,7 +188,12 @@ medRank_mat <- rank_df %>%
   column_to_rownames("prior")
 medRank_mat
 
-col_fun = colorRamp2(c(min(medRank_mat), max(medRank_mat)), c("deepskyblue4", "white"))
+col_fun = colorRamp2(
+  c(min(medRank_mat, na.rm = TRUE), mean(unlist(as.vector(medRank_mat)), na.rm = TRUE), max(medRank_mat, na.rm = TRUE)),
+  c("#4770b2", "#d6e2f2", "white")
+)
+
+#col_fun = colorRamp2(c(min(medRank_mat), max(medRank_mat)), c("deepskyblue4", "white"))
 column_ha = HeatmapAnnotation(mean_method = colMeans(medRank_mat, na.rm = T), col = list(mean_method = col_fun))
 row_ha = rowAnnotation(mean_prior = rowMeans(medRank_mat, na.rm = T), col = list(mean_prior = col_fun))