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fixed cmd running script problem for logo plots

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This commit is contained in:
Tanushree Tunstall 2021-06-24 12:12:36 +01:00
parent 552c5e77aa
commit ca2315523d
14 changed files with 206 additions and 748 deletions
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71
scripts/plotting/corr_data.R
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@ -5,28 +5,67 @@
#=======================================================================
# working dir and loading libraries
getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/")
setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd()
#source("Header_TT.R")
source("combining_dfs_plotting.R")
source("my_pairs_panel.R") # with lower panel turned off
# should return the following dfs, directories and variables
source("../functions/my_pairs_panel.R") # with lower panel turned off
source("../functions/plotting_globals.R")
source("../functions/plotting_data.R")
source("../functions/combining_dfs_plotting.R")
###########################################################
#===========
# input
#===========
#---------------------
# call: import_dirs()
#---------------------
import_dirs(drug, gene)
#---------------------------
# call: plotting_data()
#---------------------------
#if (!exists("infile_params") && exists("gene")){
if (!is.character(infile_params) && exists("gene")){ # when running as cmd
#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
cat("\nReading mcsm combined data file: ", infile_params)
mcsm_df = read.csv(infile_params, header = T)
pd_df = plotting_data(mcsm_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_metadata) && exists("gene")){ # when running as cmd
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)
# PS combined:
# 1) merged_df2
# 2) merged_df2_comp
# 3) merged_df3
# 4) merged_df3_comp
# LIG combined:
# 5) merged_df2_lig
# 6) merged_df2_comp_lig
# 7) merged_df3_lig
# 8) merged_df3_comp_lig
# 9) my_df_u
# 10) my_df_u_lig
cat(paste0("Directories imported:"
, "\ndatadir:", datadir