diff --git a/README.md b/README.md index 737549d950c78705425f6627720771d5ef3cd1e4..d156cdd449cb4a2327dd557c53fa3a70020c376e 100644 --- a/README.md +++ b/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 diff --git a/bin/miami.R b/bin/miami.R index 653a934f1c9fa37144fca147edd6f6c1afb6c724..cf03453c414057d471ed879e41ceb3299f2b30a4 100644 --- a/bin/miami.R +++ b/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(), diff --git a/fisher_for_vcf.config b/fisher_for_vcf.config index 7ed83f9fe9335ff3e8cd9643ace0745debc197b6..8605c2c85ea9a9e8557989974af30044b42ad4e8 100644 --- a/fisher_for_vcf.config +++ b/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 }