altCol=TRUE not supported anymore -> FALSE

metagenlab · Mar 3, 2020 · b93a691 · b93a691
1 parent 795f91a
commit b93a691
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Showing 6 changed files with 5 additions and 6 deletions.
diff --git a/build_n_validate_docker.sh b/build_n_validate_docker.sh
@@ -12,7 +12,6 @@ echo $3
 docker build . \
     -t metagenlab/amplicon_pipeline:$VERSION \
     -f ./Dockerfile \
-    --no-cache \
     --build-arg GITHUB_AT=$GITHUBAT \
     --build-arg TEST_CPU=$CPU && \
 docker build . \

diff --git a/ressources/r_scripts/visualization/1_Reads/dna_quant_barplots_fct.R b/ressources/r_scripts/visualization/1_Reads/dna_quant_barplots_fct.R
@@ -29,7 +29,7 @@ dna_quant_barplots_fct <- function(count_table_df, figures_save_dir, grouping_co
     ### Distinct colors
     set.seed(2)
     ColList <- unique(count_table_df[[filling_column]])
-    ColPalette <- distinctColorPalette(altCol = TRUE, k = length(unique(count_table_df[[filling_column]])))
+    ColPalette <- distinctColorPalette(altCol = FALSE, k = length(unique(count_table_df[[filling_column]])))
     names(ColPalette) = ColList
     colors_palette <- ColPalette
   }

diff --git a/ressources/r_scripts/visualization/1_Reads/qPCR_dna_quant_barplots_fct.R b/ressources/r_scripts/visualization/1_Reads/qPCR_dna_quant_barplots_fct.R
@@ -37,7 +37,7 @@ qPCR_dna_quant_barplots_fct <- function(count_table_df, figures_save_dir, groupi
     ### Distinct colors
     set.seed(2)
     ColList <- unique(count_table_df[[filling_column]])
-    ColPalette <- distinctColorPalette(altCol = TRUE, k = length(unique(count_table_df[[filling_column]])))
+    ColPalette <- distinctColorPalette(altCol = FALSE, k = length(unique(count_table_df[[filling_column]])))
     names(ColPalette) = ColList
     colors_palette <- ColPalette
   }

diff --git a/ressources/r_scripts/visualization/2_Barplots/barplots_fct.R b/ressources/r_scripts/visualization/2_Barplots/barplots_fct.R
@@ -298,7 +298,7 @@ barplots_fct <- function(melted_dataframe, sample_label, grouping_column, groupi
     else if (distinct_colors == TRUE) {
       set.seed(1)
       ColList <- unique(threshod_filtered_abs_no_zero[[t]])
-      ColPalette <- distinctColorPalette(altCol = TRUE, k = length(unique(threshod_filtered_abs_no_zero[[t]])))
+      ColPalette <- distinctColorPalette(altCol = FALSE, k = length(unique(threshod_filtered_abs_no_zero[[t]])))
       names(ColPalette) = ColList
       colors_palette <- ColPalette
 

diff --git a/ressources/r_scripts/visualization/2_Barplots/barplots_fct_filtration_at_tax_levels.R b/ressources/r_scripts/visualization/2_Barplots/barplots_fct_filtration_at_tax_levels.R
@@ -217,7 +217,7 @@ barplots_fct <- function(melted_dataframe, sample_label, grouping_column, groupi
                 else if (distinct_colors == TRUE) {
                     set.seed(8)
                     ColList <- unique(threshod_filtered_abs_no_zero[[t]])
-                    ColPalette <- distinctColorPalette(altCol = TRUE, k = length(unique(threshod_filtered_abs_no_zero[[t]])))
+                    ColPalette <- distinctColorPalette(altCol = FALSE, k = length(unique(threshod_filtered_abs_no_zero[[t]])))
                     names(ColPalette) = ColList
                     colors_palette <- ColPalette
                     colors_palette[filtering_tag] <- "#d3d3d3" # Set the filtered in balck

diff --git a/rules/5_visualization/scripts/barplot.R b/rules/5_visualization/scripts/barplot.R
@@ -239,7 +239,7 @@
                 set.seed(4)
                 ColList <- unique(threshod_filtered_abs_no_zero[[plotting_tax_ranks]])
                 print(length(unique(threshod_filtered_abs_no_zero[[plotting_tax_ranks]])))
-                ColPalette <- distinctColorPalette(altCol = TRUE, k = length(unique(threshod_filtered_abs_no_zero[[plotting_tax_ranks]])))
+                ColPalette <- distinctColorPalette(altCol = FALSE, k = length(unique(threshod_filtered_abs_no_zero[[plotting_tax_ranks]])))
                 names(ColPalette) = ColList
                 colors_palette <- ColPalette
                 colors_palette[filtering_tag] <- "#d3d3d3" # Set the filtered in balck