changes made to combining_dfs_plotting.R
This commit is contained in:
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c6d1260f74
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9 changed files with 258 additions and 126 deletions
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@ -2,11 +2,12 @@
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###########################################################
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# TASK: To combine mcsm combined file and meta data.
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# This script is sourced from other .R scripts for plotting.
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# This script is sourced by other .R scripts for plotting.
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###########################################################
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# load libraries and functions
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#source("Header_TT.R")
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#==========================================================
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# combining_dfs_plotting():
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@ -34,27 +35,6 @@ combining_dfs_plotting <- function( my_df_u
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, gene_metadata
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, lig_dist_colname = 'ligand_distance'
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, lig_dist_cutoff = 10){
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# #======================================
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# # 1: Read file: <gene>_meta data.csv
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# #======================================
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# cat("\nReading meta data file:", df1_mcsm_comb)
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#
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# my_df_u <- read.csv(df1_mcsm_comb
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# , stringsAsFactors = F
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# , header = T)
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# cat("\nDim:", dim(my_df_u))
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#
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# #======================================
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# # 2: Read file: <gene>_meta data.csv
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# #======================================
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# cat("\nReading meta data file:", df2_gene_metadata)
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#
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# gene_metadata <- read.csv(df2_gene_metadata
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# , stringsAsFactors = F
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# , header = T)
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# cat("\nDim:", dim(gene_metadata))
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#
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# table(gene_metadata$mutation_info)
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# counting NAs in AF, OR cols
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# or_mychisq
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@ -219,7 +199,6 @@ combining_dfs_plotting <- function( my_df_u
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, "\nNA in AF:", sum(is.na(merged_df3$af_kin)))
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}
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#===================================================
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# Merge3: merged_df2_comp
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# same as merge 1 but excluding NAs from ORs, etc.
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@ -273,6 +252,13 @@ combining_dfs_plotting <- function( my_df_u
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# compare dfs: foo and merged_df3_com
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all.equal(foo, bar)
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#summary(comparedf(foo, bar))
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cat("\n------------------------"
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, "\nSummary of created dfs:"
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, "\n------------------------"
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, "\n1) Dim of merged_df2: " , nrow(merged_df2), "," , ncol(merged_df2)
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, "\n2) Dim of merged_df2_comp: " , nrow(merged_df2_comp), "," , ncol(merged_df2_comp)
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, "\n3) Dim of merged_df3: " , nrow(merged_df3), "," , ncol(merged_df3)
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, "\n4) Dim of merged_df3_comp: " , nrow(merged_df3_comp), "," , ncol(merged_df3_comp))
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#####################################################################
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# Combining: LIG
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@ -281,13 +267,35 @@ combining_dfs_plotting <- function( my_df_u
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#============
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# Merges 5-8
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#============
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df_lig = my_df_u[my_df_u[[lig_dist_colname]]<lig_dist_cutoff,]
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cat("\n=========================================="
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, "\nStarting filtering for mcsm ligand df"
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, "\n===========================================")
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merged_df2_lig = merged_df2[merged_df2$ligand_distance<lig_dist_cutoff,]
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merged_df2_comp_lig = merged_df2_comp[merged_df2_comp$ligand_distance<lig_dist_cutoff,]
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if (lig_dist_colname%in%names(my_df_u)){
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cat("\nFiltering column: ", lig_dist_colname
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, "\nCut off criteria: ", lig_dist_cutoff, "Angstroms")
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df_lig = my_df_u[my_df_u[[lig_dist_colname]] < lig_dist_cutoff,]
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merged_df3_lig = merged_df3[merged_df3$ligand_distance<lig_dist_cutoff,]
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merged_df3_comp_lig = merged_df3_comp[merged_df3_comp$ligand_distance<lig_dist_cutoff,]
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#merged_df2_lig = merged_df2[merged_df2$ligand_distance<lig_dist_cutoff,]
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merged_df2_lig = merged_df2[merged_df2[[lig_dist_colname]] < lig_dist_cutoff,]
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dim(merged_df2_lig)
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merged_df2_comp_lig = merged_df2_comp[merged_df2_comp[[lig_dist_colname]] < lig_dist_cutoff,]
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merged_df3_lig = merged_df3[merged_df3[[lig_dist_colname]] < lig_dist_cutoff,]
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merged_df3_comp_lig = merged_df3_comp[merged_df3_comp[[lig_dist_colname]] < lig_dist_cutoff,]
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cat("\n------------------------"
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, "\nSummary of created ligand dfs:"
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, "\n------------------------"
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, "\n1) Dim of merged_df2_lig: " , nrow(merged_df2_lig), "," , ncol(merged_df2_lig)
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, "\n2) Dim of merged_df2_comp_lig: " , nrow(merged_df2_comp_lig), "," , ncol(merged_df2_comp_lig)
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, "\n3) Dim of merged_df3_lig: " , nrow(merged_df3_lig), "," , ncol(merged_df3_lig)
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, "\n4) Dim of merged_df3_comp_lig: " , nrow(merged_df3_comp_lig), "," , ncol(merged_df3_comp_lig))
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} else {
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cat("\nFiltering column: ", lig_dist_colname, " not found\n")
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}
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#quit()
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# sanity check
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if (nrow(merged_df3_lig) == nrow(df_lig)){
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@ -327,8 +335,13 @@ combining_dfs_plotting <- function( my_df_u
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# , "\nNo. of cols: ", ncol(get(i)), "\n")
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#}
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return(list(merged_df2, merged_df3
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, merged_df2_comp, merged_df3_comp
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, merged_df2_lig, merged_df3_lig))
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return(list( merged_df2
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, merged_df3
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, merged_df2_comp
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, merged_df3_comp
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, merged_df2_lig
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, merged_df3_lig
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, merged_df2_comp_lig
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, merged_df3_comp_lig))
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}
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@ -16,20 +16,18 @@ library(dplyr)
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## my_df_u_lig
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## dup_muts
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#========================================================
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plotting_data <- function(infile_params, mcsm_lig_cutoff = 10) {
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plotting_data <- function(df, lig_dist_colname = 'ligand_distance', lig_dist_cutoff = 10) {
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my_df = data.frame()
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my_df_u = data.frame()
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my_df_u_lig = data.frame()
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dup_muts = data.frame()
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cat(paste0("\nInput file to prepare for plotting:", infile_params, "\n") )
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#===========================
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# Read file: struct params
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#===========================
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my_df = read.csv(infile_params, header = T)
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#df = read.csv(infile_params, header = T)
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cat("\nInput dimensions:", dim(my_df))
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cat("\nInput dimensions:", dim(df))
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#==================================
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# add foldx outcome category
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@ -43,17 +41,17 @@ cat("\nInput dimensions:", dim(my_df))
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# adding foldx scaled values
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# scale data b/w -1 and 1
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#------------------------------
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n = which(colnames(my_df) == "ddg"); n
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n = which(colnames(df) == "ddg"); n
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my_min = min(my_df[,n]); my_min
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my_max = max(my_df[,n]); my_max
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my_min = min(df[,n]); my_min
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my_max = max(df[,n]); my_max
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my_df$foldx_scaled = ifelse(my_df[,n] < 0
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, my_df[,n]/abs(my_min)
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, my_df[,n]/my_max)
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df$foldx_scaled = ifelse(df[,n] < 0
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, df[,n]/abs(my_min)
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, df[,n]/my_max)
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# sanity check
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my_min = min(my_df$foldx_scaled); my_min
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my_max = max(my_df$foldx_scaled); my_max
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my_min = min(df$foldx_scaled); my_min
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my_max = max(df$foldx_scaled); my_max
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if (my_min == -1 && my_max == 1){
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cat("\nPASS: foldx ddg successfully scaled b/w -1 and 1"
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@ -67,9 +65,9 @@ if (my_min == -1 && my_max == 1){
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# adding foldx outcome category
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# ddg<0 = "Stabilising" (-ve)
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#------------------------------
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c1 = table(my_df$ddg < 0)
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my_df$foldx_outcome = ifelse(my_df$ddg < 0, "Stabilising", "Destabilising")
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c2 = table(my_df$ddg < 0)
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c1 = table(df$ddg < 0)
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df$foldx_outcome = ifelse(df$ddg < 0, "Stabilising", "Destabilising")
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c2 = table(df$ddg < 0)
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if ( all(c1 == c2) ){
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cat("\nPASS: foldx outcome successfully created")
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@ -83,19 +81,19 @@ if ( all(c1 == c2) ){
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#==================================
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# check for duplicate mutations
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if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformation)){
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if ( length(unique(df$mutationinformation)) != length(df$mutationinformation)){
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cat(paste0("\nCAUTION:", " Duplicate mutations identified"
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, "\nExtracting these...\n"))
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#cat(my_df[duplicated(my_df$mutationinformation),])
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dup_muts = my_df[duplicated(my_df$mutationinformation),]
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dup_muts = df[duplicated(df$mutationinformation),]
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dup_muts_nu = length(unique(dup_muts$mutationinformation))
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cat(paste0("\nDim of duplicate mutation df:", nrow(dup_muts)
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, "\nNo. of unique duplicate mutations:", dup_muts_nu
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, "\n\nExtracting df with unique mutations only\n"))
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my_df_u = my_df[!duplicated(my_df$mutationinformation),]
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my_df_u = df[!duplicated(df$mutationinformation),]
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}else{
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cat(paste0("\nNo duplicate mutations detected\n"))
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my_df_u = my_df
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my_df_u = df
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}
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upos = unique(my_df_u$position)
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@ -105,15 +103,14 @@ cat("\nNo. of unique mutational positions:"); cat(length(upos), "\n")
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#===============================================
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# extract mutations <10 Angstroms and symbol
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#===============================================
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table(my_df_u$ligand_distance<mcsm_lig_cutoff)
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table(my_df_u$ligand_distance<lig_dist_cutoff)
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my_df_u_lig = my_df_u[my_df_u$ligand_distance <mcsm_lig_cutoff,]
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my_df_u_lig = my_df_u[my_df_u$ligand_distance <lig_dist_cutoff,]
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cat(paste0("There are ", nrow(my_df_u_lig), " sites lying within 10\u212b of the ligand\n"))
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# return list of DFs
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#return(list(my_df, my_df_u, my_df_u_lig, dup_muts))
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my_df = df
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#df_names = c("my_df", "my_df_u", "my_df_u_lig", "dup_muts")
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all_df = list(my_df, my_df_u, my_df_u_lig, dup_muts)
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#all_df = Map(setNames, all_df, df_names)
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@ -10,21 +10,21 @@
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# input args: 'drug' and 'gene'
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# output: dir names for input and output files
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import_dirs <- function(drug, gene) {
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import_dirs <- function(drug_name, gene_name) {
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#============================
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# directories and variables
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#============================
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datadir <<- paste0("~/git/Data/")
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indir <<- paste0(datadir, drug, "/input")
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outdir <<- paste0("~/git/Data/", drug, "/output")
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plotdir <<- paste0("~/git/Data/", drug, "/output/plots")
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indir <<- paste0(datadir, drug_name, "/input")
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outdir <<- paste0("~/git/Data/", drug_name, "/output")
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plotdir <<- paste0("~/git/Data/", drug_name, "/output/plots")
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dr_muts_col <<- paste0('dr_mutations_', drug)
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other_muts_col <<- paste0('other_mutations_', drug)
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dr_muts_col <<- paste0('dr_mutations_', drug_name)
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other_muts_col <<- paste0('other_mutations_', drug_name)
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resistance_col <<- "drtype"
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gene_match <<- paste0(gene,"_p.")
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gene_match <<- paste0(gene_name,"_p.")
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}
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@ -37,20 +37,17 @@ import_dirs <- function(drug, gene) {
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#==================
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# Angstroms symbol
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#==================
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angstroms_symbol <<- "\u212b"
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#cat(paste0("There are ", nrow(my_df_u_lig), " sites lying within 10", angstroms_symbol, " of the ligand\n"))
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#===============
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# Delta symbol
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#===============
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delta_symbol <<- "\u0394"; delta_symbol
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#==========
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# Colours
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#==========
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mcsm_red2 <<- "#ae301e" # most negative
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mcsm_red1 <<- "#f8766d"
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@ -58,3 +55,4 @@ mcsm_mid <<- "white" # middle
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mcsm_blue1 <<- "#00bfc4"
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mcsm_blue2 <<- "#007d85" # most positive
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#########################################################
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@ -7,6 +7,7 @@ getwd()
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#===========================================
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source("plotting_data.R")
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infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
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pd_df = plotting_data(infile)
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my_df = pd_df[[1]]
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my_df_u = pd_df[[2]]
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# #!/usr/bin/env Rscript
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#!/usr/bin/env Rscript
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# working dir and loading libraries
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getwd()
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@ -33,14 +33,20 @@ source("plotting_globals.R")
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source("plotting_data.R")
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source("combining_dfs_plotting.R")
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gene = 'gid'
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drug = 'streptomycin'
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#---------------------
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# call: import_dirs()
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#---------------------
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import_dirs(drug, gene)
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gene = 'gid'
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drug = 'streptomycin'
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import_dirs(drug_name = drug, gene_name = gene)
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#-------------------------------
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# test function: plotting_data()
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#-------------------------------
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#============================
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# Input 1: plotting_data()
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#============================
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if (!exists("infile_params") && exists("gene")){
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#if (!is.character(infile_params) && exists("gene")){
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#in_filename_params = paste0(tolower(gene), "_all_params.csv")
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@ -49,6 +55,13 @@ if (!exists("infile_params") && exists("gene")){
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cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n")
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}
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mcsm_comb_data = read.csv(infile_params, header = T)
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pd_df = plotting_data(df = mcsm_comb_data, lig_dist_cutoff = 10)
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my_df_u = pd_df[[2]]
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#======================================
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# Input 2: read <gene>_meta data.csv
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#======================================
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if (!exists("infile_metadata") && exists("gene")){
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#if (!is.character(infile_params) && exists("gene")){{
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in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
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@ -56,18 +69,6 @@ if (!exists("infile_metadata") && exists("gene")){
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cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
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}
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#============================
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# Input 1: plotting_data()
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#============================
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#---------------------
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# call: plotting_data()
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#---------------------
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pd_df = plotting_data(infile_params)
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my_df = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
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#======================================
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# Input 2: read <gene>_meta data.csv
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#======================================
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cat("\nReading meta data file:", infile_metadata)
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gene_metadata <- read.csv(infile_metadata
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@ -85,3 +86,5 @@ merged_df2_comp = all_plot_dfs[[3]]
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merged_df3_comp = all_plot_dfs[[4]]
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merged_df2_lig = all_plot_dfs[[5]]
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merged_df3_lig = all_plot_dfs[[6]]
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merged_df2_comp_lig = all_plot_dfs[[7]]
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merged_df3_comp_lig = all_plot_dfs[[8]]
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@ -7,6 +7,7 @@
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# install.packages("gplots", dependencies = TRUE)
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# library(gplots)
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#}
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require("getopt", quietly = TRUE) # cmd parse arguments
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if (!require("tidyverse")) {
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install.packages("tidyverse", dependencies = TRUE)
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@ -10,15 +10,66 @@ setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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source("Header_TT.R")
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#library(ggplot2)
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#library(data.table)
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#library(dplyr)
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source("../functions/plotting_globals.R")
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source("../functions/plotting_data.R")
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source("../functions/combining_dfs_plotting.R")
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###########################################################
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# command line args
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#********************
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drug = 'streptomycin'
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gene = 'gid'
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#===========
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# input
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#===========
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source("combining_dfs_plotting.R")
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#---------------------
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# call: import_dirs()
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#---------------------
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import_dirs(drug, gene)
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#---------------------------
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# call: plotting_data()
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#---------------------------
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if (!exists("infile_params") && exists("gene")){
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#if (!is.character(infile_params) && exists("gene")){
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#in_filename_params = paste0(tolower(gene), "_all_params.csv")
|
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in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
|
||||
infile_params = paste0(outdir, "/", in_filename_params)
|
||||
cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n")
|
||||
}
|
||||
|
||||
# Input 1: read <gene>_comb_afor.csv
|
||||
pd_df = plotting_data(infile_params)
|
||||
my_df_u = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
|
||||
|
||||
#--------------------------------
|
||||
# call: combining_dfs_plotting()
|
||||
#--------------------------------
|
||||
if (!exists("infile_metadata") && exists("gene")){
|
||||
#if (!is.character(infile_params) && exists("gene")){{
|
||||
in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
|
||||
infile_metadata = paste0(outdir, "/", in_filename_metadata)
|
||||
cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
|
||||
}
|
||||
|
||||
# Input 2: read <gene>_meta data.csv
|
||||
cat("\nReading meta data file:", infile_metadata)
|
||||
|
||||
gene_metadata <- read.csv(infile_metadata
|
||||
, stringsAsFactors = F
|
||||
, header = T)
|
||||
|
||||
all_plot_dfs = combining_dfs_plotting(my_df_u
|
||||
, gene_metadata
|
||||
, lig_dist_colname = 'ligand_distance'
|
||||
, lig_dist_cutoff = 10)
|
||||
|
||||
#merged_df2 = all_plot_dfs[[1]]
|
||||
merged_df3 = all_plot_dfs[[2]]
|
||||
#merged_df2_comp = all_plot_dfs[[3]]
|
||||
#merged_df3_comp = all_plot_dfs[[4]]
|
||||
#merged_df2_lig = all_plot_dfs[[5]]
|
||||
#merged_df3_lig = all_plot_dfs[[6]]
|
||||
#===========
|
||||
# output
|
||||
#===========
|
||||
|
|
@ -32,12 +83,6 @@ plot_logo_combined_labelled = paste0(plotdir,"/", logo_combined_labelled)
|
|||
# REASSIGNMENT
|
||||
my_df = merged_df3
|
||||
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
# clear excess variables
|
||||
rm(merged_df2, merged_df2_comp, merged_df2_lig, merged_df2_comp_lig
|
||||
, merged_df3_comp, merged_df3_comp_lig
|
||||
, my_df_u, my_df_u_lig, merged_df3_lig)
|
||||
|
||||
colnames(my_df)
|
||||
str(my_df)
|
||||
|
||||
|
|
@ -166,8 +211,8 @@ p3 = p2 +
|
|||
theme(legend.position = "bottom"
|
||||
#, legend.title = element_blank()
|
||||
, legend.title = element_text("Amino acid properties", size = 20)
|
||||
, legend.text = element_text( size = 20)
|
||||
, axis.text.x = element_text(size = 20, angle = 90)
|
||||
, legend.text = element_text(size = 20)
|
||||
, axis.text.x = element_text(size = 16, angle = 90)
|
||||
, axis.text.y = element_blank()
|
||||
, axis.title.y = element_blank()
|
||||
, axis.title.x = element_text(size = 22))+
|
||||
|
|
@ -237,7 +282,7 @@ position_or = as.numeric(colnames(wide_df_or))
|
|||
#============================================
|
||||
# custom height (OR) logo plot: yayy works
|
||||
logo_or = ggseqlogo(wide_df_or, method="custom", seq_type="aa") + ylab("my custom height") +
|
||||
theme(axis.text.x = element_text(size = 16
|
||||
theme(axis.text.x = element_text(size = 15
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
|
|
|
|||
|
|
@ -10,14 +10,66 @@ setwd("~/git/LSHTM_analysis/scripts/plotting")
|
|||
getwd()
|
||||
|
||||
source("Header_TT.R")
|
||||
#library(ggplot2)
|
||||
#library(data.table)
|
||||
#library(dplyr)
|
||||
source("../functions/plotting_globals.R")
|
||||
source("../functions/plotting_data.R")
|
||||
source("../functions/combining_dfs_plotting.R")
|
||||
###########################################################
|
||||
# command line args
|
||||
#********************
|
||||
drug = 'streptomycin'
|
||||
gene = 'gid'
|
||||
|
||||
#===========
|
||||
# input
|
||||
#===========
|
||||
source("combining_dfs_plotting.R")
|
||||
#---------------------
|
||||
# call: import_dirs()
|
||||
#---------------------
|
||||
import_dirs(drug, gene)
|
||||
|
||||
#---------------------------
|
||||
# call: plotting_data()
|
||||
#---------------------------
|
||||
if (!exists("infile_params") && exists("gene")){
|
||||
#if (!is.character(infile_params) && exists("gene")){
|
||||
#in_filename_params = paste0(tolower(gene), "_all_params.csv")
|
||||
in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
|
||||
infile_params = paste0(outdir, "/", in_filename_params)
|
||||
cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n")
|
||||
}
|
||||
|
||||
# Input 1: read <gene>_comb_afor.csv
|
||||
pd_df = plotting_data(infile_params)
|
||||
my_df_u = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
|
||||
|
||||
#--------------------------------
|
||||
# call: combining_dfs_plotting()
|
||||
#--------------------------------
|
||||
if (!exists("infile_metadata") && exists("gene")){
|
||||
#if (!is.character(infile_params) && exists("gene")){{
|
||||
in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
|
||||
infile_metadata = paste0(outdir, "/", in_filename_metadata)
|
||||
cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
|
||||
}
|
||||
|
||||
# Input 2: read <gene>_meta data.csv
|
||||
cat("\nReading meta data file:", infile_metadata)
|
||||
|
||||
gene_metadata <- read.csv(infile_metadata
|
||||
, stringsAsFactors = F
|
||||
, header = T)
|
||||
|
||||
all_plot_dfs = combining_dfs_plotting(my_df_u
|
||||
, gene_metadata
|
||||
, lig_dist_colname = 'ligand_distance'
|
||||
, lig_dist_cutoff = 10)
|
||||
|
||||
#merged_df2 = all_plot_dfs[[1]]
|
||||
merged_df3 = all_plot_dfs[[2]]
|
||||
#merged_df2_comp = all_plot_dfs[[3]]
|
||||
#merged_df3_comp = all_plot_dfs[[4]]
|
||||
#merged_df2_lig = all_plot_dfs[[5]]
|
||||
#merged_df3_lig = all_plot_dfs[[6]]
|
||||
|
||||
#===========
|
||||
# output
|
||||
|
|
@ -32,12 +84,6 @@ plot_logo_multiple_muts = paste0(plotdir,"/", logo_multiple_muts)
|
|||
# REASSIGNMENT
|
||||
my_df = merged_df3
|
||||
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
# clear excess variables
|
||||
rm(merged_df2, merged_df2_comp, merged_df2_lig, merged_df2_comp_lig
|
||||
, merged_df3_comp, merged_df3_comp_lig
|
||||
, my_df_u, my_df_u_lig, merged_df3_lig)
|
||||
|
||||
colnames(my_df)
|
||||
str(my_df)
|
||||
|
||||
|
|
@ -117,7 +163,7 @@ p0
|
|||
p1 = p0 + theme(legend.position = "none"
|
||||
, legend.title = element_blank()
|
||||
, legend.text = element_text(size = 20)
|
||||
, axis.text.x = element_text(size = 20, angle = 90)
|
||||
, axis.text.x = element_text(size = 17, angle = 90)
|
||||
, axis.text.y = element_blank())
|
||||
p1
|
||||
|
||||
|
|
@ -138,7 +184,6 @@ rownames(tab_wt)
|
|||
|
||||
#**************
|
||||
# Plot 2: wild_type logo
|
||||
|
||||
#**************
|
||||
# sanity check: MUST BE TRUE
|
||||
|
||||
|
|
@ -164,8 +209,8 @@ p3 = p2 +
|
|||
theme(legend.position = "bottom"
|
||||
#, legend.title = element_blank()
|
||||
, legend.title = element_text("Amino acid properties", size = 20)
|
||||
, legend.text = element_text( size = 20)
|
||||
, axis.text.x = element_text(size = 20, angle = 90)
|
||||
, legend.text = element_text(size = 20)
|
||||
, axis.text.x = element_text(size = 17, angle = 90)
|
||||
, axis.text.y = element_blank()
|
||||
, axis.title.x = element_text(size = 22))+
|
||||
|
||||
|
|
|
|||
45
scripts/plotting/logo_plot.R
Normal file → Executable file
45
scripts/plotting/logo_plot.R
Normal file → Executable file
|
|
@ -15,9 +15,36 @@ source("../functions/combining_dfs_plotting.R")
|
|||
###########################################################
|
||||
# command line args
|
||||
#********************
|
||||
drug = 'streptomycin'
|
||||
gene = 'gid'
|
||||
#drug = 'streptomycin'
|
||||
#gene = 'gid'
|
||||
#********************
|
||||
# !!!FUTURE TODO!!!
|
||||
# Can pass additional params of output/plot dir by user.
|
||||
# Not strictly required for my workflow since it is optimised
|
||||
# to have a streamlined input/output flow without filename worries.
|
||||
#********************
|
||||
spec = matrix(c(
|
||||
"drug" , "d", 1, "character",
|
||||
"gene" , "g", 1, "character",
|
||||
"data_file1" , "fa", 2, "character",
|
||||
"data_file2" , "fb", 2, "character"
|
||||
), byrow = TRUE, ncol = 4)
|
||||
|
||||
opt = getopt(spec)
|
||||
|
||||
#FIXME: detect if script running from cmd, then set these
|
||||
drug = opt$drug
|
||||
gene = opt$gene
|
||||
infile_params = opt$data_file1
|
||||
infile_metadata = opt$data_file2
|
||||
|
||||
# hardcoding when not using cmd
|
||||
#drug = "streptomycin"
|
||||
#gene = "gid"
|
||||
|
||||
if(is.null(drug)|is.null(gene)) {
|
||||
stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
|
||||
}
|
||||
#===========
|
||||
# input
|
||||
#===========
|
||||
|
|
@ -29,8 +56,8 @@ import_dirs(drug, gene)
|
|||
#---------------------------
|
||||
# call: plotting_data()
|
||||
#---------------------------
|
||||
if (!exists("infile_params") && exists("gene")){
|
||||
#if (!is.character(infile_params) && exists("gene")){
|
||||
#if (!exists("infile_params") && exists("gene")){
|
||||
if (!is.character(infile_params) && exists("gene")){
|
||||
#in_filename_params = paste0(tolower(gene), "_all_params.csv")
|
||||
in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
|
||||
infile_params = paste0(outdir, "/", in_filename_params)
|
||||
|
|
@ -38,14 +65,15 @@ if (!exists("infile_params") && exists("gene")){
|
|||
}
|
||||
|
||||
# Input 1: read <gene>_comb_afor.csv
|
||||
pd_df = plotting_data(infile_params)
|
||||
my_df = read.csv(infile_params, header = T)
|
||||
pd_df = plotting_data(my_df)
|
||||
my_df_u = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
|
||||
|
||||
#--------------------------------
|
||||
# call: combining_dfs_plotting()
|
||||
#--------------------------------
|
||||
if (!exists("infile_metadata") && exists("gene")){
|
||||
#if (!is.character(infile_params) && exists("gene")){{
|
||||
#if (!exists("infile_metadata") && exists("gene")){
|
||||
if (!is.character(infile_params) && exists("gene")){
|
||||
in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
|
||||
infile_metadata = paste0(outdir, "/", in_filename_metadata)
|
||||
cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
|
||||
|
|
@ -63,7 +91,7 @@ all_plot_dfs = combining_dfs_plotting(my_df_u
|
|||
, lig_dist_colname = 'ligand_distance'
|
||||
, lig_dist_cutoff = 10)
|
||||
|
||||
merged_df2 = all_plot_dfs[[1]]
|
||||
#merged_df2 = all_plot_dfs[[1]]
|
||||
merged_df3 = all_plot_dfs[[2]]
|
||||
#merged_df2_comp = all_plot_dfs[[3]]
|
||||
#merged_df3_comp = all_plot_dfs[[4]]
|
||||
|
|
@ -146,6 +174,7 @@ wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
|
|||
|
||||
wide_df_or = as.matrix(wide_df_or)
|
||||
rownames(wide_df_or) = wide_df_or[,1]
|
||||
dim(wide_df_or)
|
||||
wide_df_or = wide_df_or[,-1]
|
||||
str(wide_df_or)
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue