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moved combining_dfs_plotting.R to function and added test script for this as well

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Tanushree Tunstall 2021-06-22 18:15:15 +01:00
parent ac383165ec
commit 13c61e7813
5 changed files with 100 additions and 9 deletions
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0
scripts/plotting/combining_dfs_plotting.R → scripts/functions/combining_dfs_plotting.R
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4
scripts/functions/test_aa_prop_bp.R
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@ -2,14 +2,14 @@ library(ggplot2)
library(tidyverse)
library(data.table)
setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
setwd("~/git/LSHTM_analysis/scripts/functions/")
getwd()
#############################################################
#===========================================
# load functions, data, dirs, hardocded vars
# that will be used in testing the functions
#===========================================
source("../plotting_data.R")
source("plotting_data.R")
infile = "/home/tanu/git/Data/streptomycin/output/"
pd_df = plotting_data(infile)
my_df = pd_df[[1]]

10
scripts/functions/test_af_or_calcs.R
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@ -7,11 +7,15 @@
#source("Header_TT.R")
require("getopt", quietly = TRUE) # cmd parse arguments
# working dir and loading libraries
getwd()
setwd("~/git/LSHTM_analysis/scripts/functions/")
getwd()
# load functions
source("functions/plotting_globals.R")
source("functions/mychisq_or.R")
source("functions/myaf_or_calcs.R")
source("plotting_globals.R")
source("mychisq_or.R")
source("myaf_or_calcs.R")
# cmd options + sensible defaults
drug = "streptomycin"

6
scripts/functions/test_bp.R
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@ -1,11 +1,11 @@
setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
setwd("~/git/LSHTM_analysis/scripts/functions/")
getwd()
#############################################################
#===========================================
# load functions, data, dirs, hardocded vars
# that will be used in testing the functions
#===========================================
source("../plotting_data.R")
source("plotting_data.R")
infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
pd_df = plotting_data(infile)
my_df = pd_df[[1]]
@ -13,7 +13,7 @@ my_df_u = pd_df[[2]]
my_df_u_lig = pd_df[[3]]
dup_muts = pd_df[[4]]
source("../plotting_globals.R")
source("plotting_globals.R")
drug = "streptomycin"
gene = "gid"

87
scripts/functions/test_combining_dfs_plotting.R Normal file
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@ -0,0 +1,87 @@
# #!/usr/bin/env Rscript
# working dir and loading libraries
getwd()
setwd("~/git/LSHTM_analysis/scripts/functions/")
getwd()
# infile_params = paste0(outdir, "/" , tolower(gene), "_comb_afor.csv")
# infile_metadata = paste0(outdir, "/", tolower(gene), "_metadata")
#
#
# source("combining_dfs_plotting_func.R")
#
####################################################################
# in_file_params = "~/git/Data/streptomycin/output/gid_comb_afor.csv"
# in_file_metadata = "~/git/Data/streptomycin/output/gid_metadata.csv"
#
# all_plot_dfs = combining_dfs_plotting(df1_mcsm_comb = infile_params
# , df2_gene_metadata = infile_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]]
#
# bar_colnames = data.frame(colnames(merged_df2))
###########################################################
source("plotting_globals.R")
source("plotting_data.R")
source("combining_dfs_plotting.R")
gene = 'gid'
drug = 'streptomycin'
#---------------------
# call: import_dirs()
#---------------------
import_dirs(drug, 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)
cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n")
}
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 1: plotting_data()
#============================
#---------------------
# call: plotting_data()
#---------------------
pd_df = plotting_data(infile_params)
my_df = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
#======================================
# 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]]