feat: include color palette in tx_type_palette

R/functions.R

@@ -288,7 +288,7 @@ plot_log2FC <- function(DEG_DET_table, selected_gene, custom_colors = NULL) {
       )
     ) +
       ggplot2::geom_bar(stat = "identity") +
-      ggplot2::scale_fill_manual(values = tx_type_color_names) +
+      ggplot2::scale_fill_manual(values = tx_type_palette()) +
       ggplot2::theme_bw()
   } else {
     plot_obj <- ggplot2::ggplot(
@@ -301,9 +301,28 @@ plot_log2FC <- function(DEG_DET_table, selected_gene, custom_colors = NULL) {
       )
     ) +
       ggplot2::geom_bar(stat = "identity") +
-      ggplot2::scale_fill_manual(values = tx_type_color_names) +
+      ggplot2::scale_fill_manual(values = tx_type_palette()) +
       ggplot2::theme_bw()
   }
   return(plot_obj)
   # ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 0.5))
 }
+
+tx_type_palette <- function() {
+  fixed_tx_biotypes <- c(
+    "gene", "protein_coding", "retained_intron",
+    "processed_transcript", "nonsense_mediated_decay",
+    "lncRNA", "processed_pseudogene",
+    "transcribed_unprocessed_pseudogene",
+    "unprocessed_pseudogene", "non_stop_decay", "transcribed_unitary_pseudogene",
+    "pseudogene", "unitary_pseudogene"
+  )
+  tx_type_color_names <- c(
+    "#fb8072", "#a6d854", "#8da0cb", "#fc8d62",
+    "#66c2a5", "#e78ac3", "#ffd92f", "#e5c494",
+    "#d9d9d9", "#d9d9d9", "#d9d9d9", "#ffffb3",
+    "#d9d9d9"
+  )
+  names(tx_type_color_names) <- fixed_tx_biotypes
+  return(tx_type_color_names)
+}

R/plot_tx_context.R

@@ -77,8 +77,8 @@ plot_tx_context <- function(
       ),
       color = NA
     ) +
-    ggplot2::scale_fill_manual(values = tx_type_color_names) +
-    ggplot2::scale_color_manual(values = tx_type_color_names) +
+    ggplot2::scale_fill_manual(values = tx_type_palette()) +
+    ggplot2::scale_color_manual(values = tx_type_palette()) +
     ggplot2::geom_segment(
       mapping = ggplot2::aes(
         x = segment_start,

R/profile_plot.R

@@ -95,7 +95,7 @@ plot_tx_expr <- function(genes_to_plot, profile_data) {
       size = 3, shape = 21
     ) +
     ggplot2::scale_alpha_manual(values = transparency_vector) +
-    ggplot2::scale_color_manual(values = tx_type_color_names, aesthetics = c("color", "fill")) +
+    ggplot2::scale_color_manual(values = tx_type_palette(), aesthetics = c("color", "fill")) +
     # ggplot2::theme_bw()
     ggpubr::theme_pubr() +
     ggplot2::theme(legend.position = "right") +

vignettes/isoformic_intro.Rmd

@@ -328,7 +328,8 @@ This table will represent cases which could be characterized as isoform switches
 
 Before we start plotting we will define a general set of colors to be used through the entire pipeline associated with a certain type of transcript. Here we colored all the most abundant types separately and the less abundant on the same grey tone and name that vector accordingly
 
-```{r}
+```{r, eval=FALSE}
+# TODO: @luciorq Check implementation of function `tx_type_palette()`
 fixed_tx_biotypes <- c(
   "gene", "protein_coding", "retained_intron",
   "processed_transcript", "nonsense_mediated_decay",