Mercurial > repos > proteore > proteore_maps_visualization
comparison kegg_maps_visualization.R @ 10:a4db9efe1e43 draft
"planemo upload commit 78a50fa16dcea6afd93a2f4de17ed193a2aa7dd3-dirty"
| author | proteore |
|---|---|
| date | Mon, 02 Mar 2020 09:23:05 +0000 |
| parents | 9ac0ade20b3f |
| children | 7d04efde2526 |
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| 9:9ac0ade20b3f | 10:a4db9efe1e43 |
|---|---|
| 173 | 173 |
| 174 get_limit <- function(mat) { | 174 get_limit <- function(mat) { |
| 175 min = min(apply(mat,2,min)) | 175 min = min(apply(mat,2,min)) |
| 176 max = max(apply(mat,2,max)) | 176 max = max(apply(mat,2,max)) |
| 177 return(c(min,max)) | 177 return(c(min,max)) |
| 178 } | |
| 179 | |
| 180 check_pathway_ids<- function(pathways_ids) { | |
| 181 problematic_pathways <- c("04215","04723") | |
| 182 to_remove <- intersect(pathways_ids,problematic_pathways) | |
| 183 if (length(to_remove) > 0){ print(paste("Pathway(s)",to_remove,"have been remove from input")) } | |
| 184 pathways_ids <- pathways_ids[which(!pathways_ids %in% problematic_pathways)] | |
| 185 if (length(pathways_ids) == 0){stop("No pathways ids to process")} | |
| 186 return (pathways_ids) | |
| 178 } | 187 } |
| 179 | 188 |
| 180 get_args <- function(){ | 189 get_args <- function(){ |
| 181 | 190 |
| 182 ## Collect arguments | 191 ## Collect arguments |
| 236 header2 <- str2bool(args$header2) | 245 header2 <- str2bool(args$header2) |
| 237 pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col)) | 246 pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col)) |
| 238 pathways_file = read_file(args$pathways_input,header2) | 247 pathways_file = read_file(args$pathways_input,header2) |
| 239 ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) | 248 ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) |
| 240 } | 249 } |
| 241 if (args$native_kegg) { ids <- ids[ids != "04215"] } | 250 if (args$native_kegg) {ids = check_pathway_ids(ids)} #remove problematic pathways |
| 242 pathways_list <- read_file(args$pathways_list,F) | 251 pathways_list <- read_file(args$pathways_list,F) |
| 243 if (!is.null(args$id_list)) { | 252 if (!is.null(args$id_list)) { |
| 244 id_list <- get_list_from_cp(args$id_list) | 253 id_list <- get_list_from_cp(args$id_list) |
| 245 } | 254 } |
| 246 id_type <- tolower(args$id_type) | 255 id_type <- tolower(args$id_type) |