release v_2.1: Miamiplot improved for right display of the color legend

README.md

@@ -260,6 +260,11 @@ Gitlab developers
 ## WHAT'S NEW IN
 
 
+### v2.1
+
+Miamiplot improved for right display of the color legend
+
+
 ### v2.0
 
 Code debugged because it was overwritting the ipunt file if named res.vcf.gz

bin/miami.R

@@ -514,7 +514,7 @@ if(empty.obs == TRUE){
     assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), theme_bw())
     assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), theme(
         plot.title = ggplot2::element_text(size = 8), 
-        legend.position=if(is.null(bottom.y.column)){"none"},
+        legend.position=if(is.null(color.column)){"none"},
         panel.border = element_blank(),
         panel.grid.major.x = element_blank(),
         panel.grid.minor.x = element_blank(),
@@ -559,7 +559,7 @@ if(empty.obs == TRUE){
         ))
         assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), theme_bw())
         assign(paste0(tempo.gg.name2, tempo.gg.count2 <- tempo.gg.count2 + 1), theme(
-            # legend.position="none", # this is to remove the graduit legend that is already present in the top graphic. Inactivated since I have to keep this legend to have x-axis alignment of the 2 plots
+            legend.position=if(is.null(color.column)){"none"},
             panel.border = element_blank(),
             panel.grid.major.x = element_blank(),
             panel.grid.minor.x = element_blank(),

fisher_for_vcf.config

@@ -25,7 +25,7 @@ env {
     tsv_extra_fields = "AC AF CSQ_SIFT CSQ_PolyPhen" // subfields from INFO to add as columns in the tsv file. Example: tsv_extra_fields = "AC AF". Write "CSQ_PolyPhen" for a sub field of the CSQ field of INFO. Write "NULL" if not required. Warning: use a single space between string
     x_lim = "chr1" // x-axis limits. Either "whole" for the whole genome, "region" to have the regions of the region parameter (i.e., "whole" if region == "none"), or a character string written like the region parameter, to have the x-axis limited to the x_lim parameter. Write "NULL" to does not plot results
     bottom_y_column = "AF" // any of the OR, P_VALUE, NEG_LOG10_P_VALUE or PATIENT_NB column of the res.tsv file for the y-axis of the bottom manhattan plot -> miami plot. Can also be an added column through the tsv_extra_fields parameter. Indicated column of field must be quantitative. Write "NULL" to get the res.tsv file. Then, explore the columns before rerunning the nextflow process using - resume. "NULL" generates a simple manhattan plot
-    color_column = "AF" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
+    color_column = "NULL" // as for bottom_y_column in order color the dots. Write "NULL" if not required (dots will be alternatively grey and blue, according to chromo order)
     y_lim1 = 3 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Write "NULL" for no particular limit
     y_lim2 = 2 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5. Not considered if bottom_y_column = "NULL"
     cute_path = "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
@@ -162,13 +162,13 @@ process {
     // all the processes of the main.nf file with the label 'bedtools' will use this directives by default
     withLabel: bash {
         container='gmillot/htslib_v1.0:gitlab_v9.1'
-        cpus=16 // only used when name = "local" in the executor part above
+        cpus=1 // only used when name = "local" in the executor part above
         memory='64G' // only used when name = "local" in the executor part above
     }
 
     withLabel: python {
         container='gmillot/python_v3.9.10_extended_v3.1:gitlab_v8.7'
-        cpus=16 // only used when name = "local" in the executor part above
+        cpus=1 // only used when name = "local" in the executor part above
         memory='64G' // only used when name = "local" in the executor part above
     }