release v1.1: Miami plot improvement

README.md

@@ -232,6 +232,11 @@ Gitlab developers
 <br /><br />
 ## WHAT'S NEW IN
 
+### v1.1
+
+1) Miami plot improvement
+
+
 ### v1.0
 
 1) everything

bin/miami.R

@@ -75,6 +75,7 @@ if(interactive() == FALSE){ # if(grepl(x = commandArgs(trailingOnly = FALSE), pa
         "fisher", 
         "chr", 
         "y.lim1", 
+        "x.lim", 
         "y.lim2",
         "cute", 
         "log"
@@ -102,11 +103,23 @@ rm(tempo.cat)
 
 # fisher <- "C:/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/fisher.tsv"
 # chr <- "C:/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/hg19_grch37p5_chr_size_cumul.txt"
+# x.lim <- "whole"
 # y.lim1 <- 5
 # y.lim2 <- 3
 # cute <- "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R" 
 # log <- "report.txt"
 
+fisher <- "C:/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/fisher.tsv"
+chr <- "C:/Users/gael/Documents/Git_projects/08002_bourgeron/dataset/hg19_grch37p5_chr_size_cumul.txt"
+x.lim <- "whole"
+y.lim1 <- 5 
+y.lim2 <- 3
+cute <- "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.4.0/cute_little_R_functions.R" 
+log <- "report.txt"
+
+
+
+
 ################################ end Test
 
 ################################ Recording of the initial parameters
@@ -120,6 +133,7 @@ param.list <- c(
     if(run.way == "SCRIPT"){"command"}, 
     "fisher", 
     "chr", 
+    "x.lim",
     "y.lim1", 
     "y.lim2",
     "cute", 
@@ -225,6 +239,7 @@ ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text
 tempo <- fun_check(data = fisher, class = "vector", typeof = "character", length = 1) ; eval(ee)
 tempo <- fun_check(data = chr, class = "vector", typeof = "character", length = 1) ; eval(ee)
 # tempo <- fun_check(data = cute, class = "vector", typeof = "character", length = 1) ; eval(ee) # check above
+tempo <- fun_check(data = x.lim, options = c("whole", "region"), length = 1) ; eval(ee)
 if(length(y.lim1) != 1 & any(grepl(y.lim1, pattern = "\\D"))){# normally no NA with is.null()
     tempo.cat <- paste0("ERROR IN global_logo.R:\nTHE y_lim1 PARAMETER MUST BE A SINGLE INTEGER\nHERE IT IS: \n", paste0(y.lim1, collapse = " "))
     stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
@@ -249,6 +264,7 @@ if(any(arg.check) == TRUE){ # normally no NA
 tempo.arg <-c(
     "fisher",
     "chr", 
+    "x.lim", 
     "y.lim1", 
     "y.lim2",
     "log"
@@ -354,6 +370,11 @@ if(length(obs) > 0 & nrow(obs) > 0){
     for(i1 in chr$CHR_NB){
         obs$coord[obs$chr == i1] <- obs$position[obs$chr == i1] + chr$LENGTH_CUMUL_TO_ADD[i1]
     }
+    if(x.lim == "region"){
+        any(grepl(x = obs$chr, pattern = "^MT$|^M$")))
+        strsplit()
+
+    }
 }else{
     tempo.warn <- paste0("EMPTY fisher FILE: NO PLOT DRAWN")
     fun_report(data = paste0("WARNING\n", tempo.warn), output = log, path = "./", overwrite = FALSE)

fisher_for_vcf.config

@@ -22,6 +22,7 @@ env {
     chr_path = "/mnt/c/Users/Gael/Documents/Git_projects/fisher_for_vcf/dataset/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
     //chr_path = "/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/human hg19_grch37/hg19_grch37p5_chr_size_cumul.txt" // human chromo infos
     region = "chr1" // region to parse. Write "chr7:0-147000000, chr10:1000000-2000000" for a single region, "chr7:0-147000000, chr10:1000000-2000000" if two regions, ""chr7" for a whole chromosome, "chr7, chr1" for two chromosomes and "None" for the complete genome // Warning : replace eval() by ast.literal_eval() from ast package in the main py code ?
+    x_lim = "whole" // x-axis limits. Either "whole" for the whole genome, or "region" to have the x-axis limited to the region parameter
     y_lim1 = 5 // max y-axis limit of the top panel in the miami plot, in log10, i.e., 5 means up to score 10^5
     y_lim2 = 20 // max y-axis limit of the bottom panel in the miami plot, in log10, i.e., 5 means up to score 10^5
     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"
@@ -46,12 +47,8 @@ result_folder_name = "PL_family_WGS_fisher"
 
 //// slurm variables
 // see https://confluence.pasteur.fr/pages/viewpage.action?pageId=69304504
-fastqueue = 'common,dedicated' // fast for -p option of slurm. Example: fastqueue = 'common,dedicated'. Example: fastqueue = 'hubbioit'
-fastqos = '--qos=ultrafast' // fast for --qos option of slurm. Example: fastqos= '--qos=fast'
-normalqueue = 'hubbioit' // normal for -p option of slurm. Example: normalqueue = 'bioevo'
-normalqos = '--qos=hubbioit' // normal for --qos option of slurm. Example: normalqos = '--qos=dedicated'
-longqueue = 'hubbioit' // slow for -p option of slurm. Example: longqueue = 'bioevo'
-longqos = '--qos=hubbioit' // slow for --qos option of slurm. Example: longqos = '--qos=dedicated'
+queue = 'common,dedicated' // -p option of slurm. Example: queue = 'common,dedicated'. Example: queue = 'hubbioit'
+qos = '--qos=ultrafast' // --qos option of slurm. Example: qos= '--qos=fast'. Example: qos = '--qos=ultrafast'. Example: qos = '--qos=hubbioit'
 add_options = ' ' // additional option of slurm. Example: addoptions = '--exclude=maestro-1101,maestro-1034' or add_options = ' '
 //// end slurm variables
 
@@ -146,8 +143,8 @@ process {
 // directives for all the processes
     // executor='local' // no need because already defined above in the executor scope
     if(system_exec == 'slurm'){
-        queue = "$longqueue"
-        clusterOptions = "$longqos $add_options"
+        queue = "$queue"
+        clusterOptions = "$qos $add_options"
         scratch=false
         maxRetries=30
         errorStrategy='retry'

fisher_for_vcf.nf

@@ -166,6 +166,7 @@ process miamiplot {
     input:
     file fisher from fisher_ch3
     file chr from chr_ch
+    val x_lim
     val y_lim1
     val y_lim2
     file cute_file
@@ -177,7 +178,7 @@ process miamiplot {
     script:
     """
     #!/bin/bash -ue
-    miami.R ${fisher} ${chr} "${y_lim1}" "${y_lim2}" "${cute_file}" "miami_report.txt"
+    miami.R ${fisher} ${chr} "${x_lim}" "${y_lim1}" "${y_lim2}" "${cute_file}" "miami_report.txt"
     """
 
 }