comparison kegg_maps_visualization.R @ 6:eb140217a9f1 draft default tip

"planemo upload commit 1f9a98db2496834cc38a281cbe3d4b11de2bc3d2-dirty"

5:4a3056be0774

  }
  return(res)
}

get_limit <- function(mat) {
  min = min(apply(mat,2,min))
  max = max(apply(mat,2,max))
  return(c(min,max))
}

get_args <- function(){
  
  ## Collect arguments

    header2 <- str2bool(args$header2)
    pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col))
    pathways_file = read_file(args$pathways_input,header2)
    ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
  }
  if (args$native_kegg) { ids <- ids[ids != "04215"] }
  pathways_list <- read_file(args$pathways_list,F)
  if (!is.null(args$id_list)) {
    id_list <- get_list_from_cp(args$id_list)
    }
  id_type <- tolower(args$id_type)

6:eb140217a9f1

  }
  return(res)
}

get_limit <- function(mat) {
  min = min(apply(mat,2,min,na.rm=TRUE))
  max = max(apply(mat,2,max,na.rm=TRUE))
  return(c(min,max))
}

check_pathway_ids<- function(pathways_ids) {
  problematic_pathways <- c("04215","04723")
  to_remove <- intersect(pathways_ids,problematic_pathways)
  if (length(to_remove) > 0){ print(paste("Pathway(s)",to_remove,"have been remove from input")) }
  pathways_ids <- pathways_ids[which(!pathways_ids %in% problematic_pathways)]
  if (length(pathways_ids) == 0){stop("No pathways ids to process")}
  return (pathways_ids)
}

get_args <- function(){
  
  ## Collect arguments

    header2 <- str2bool(args$header2)
    pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col))
    pathways_file = read_file(args$pathways_input,header2)
    ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
  }
  if (args$native_kegg) {ids = check_pathway_ids(ids)} #remove problematic pathways
  pathways_list <- read_file(args$pathways_list,F)
  if (!is.null(args$id_list)) {
    id_list <- get_list_from_cp(args$id_list)
    }
  id_type <- tolower(args$id_type)