tanu/LSHTM_analysis
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generated logo_plot.R from cmd, checked

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Tanushree Tunstall 2021-06-23 16:35:44 +01:00
parent 7e6affea84
commit 8f4daba98d
1 changed files with 7 additions and 11 deletions
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14
scripts/plotting/logo_plot.R
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@ -57,7 +57,7 @@ import_dirs(drug, gene)
# call: plotting_data() # call: plotting_data()
#--------------------------- #---------------------------
#if (!exists("infile_params") && exists("gene")){ #if (!exists("infile_params") && exists("gene")){
if (!is.character(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), "_all_params.csv")
in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
infile_params = paste0(outdir, "/", in_filename_params) infile_params = paste0(outdir, "/", in_filename_params)
@ -65,15 +65,16 @@ if (!is.character(infile_params) && exists("gene")){
} }
# Input 1: read <gene>_comb_afor.csv # Input 1: read <gene>_comb_afor.csv
my_df = read.csv(infile_params, header = T) cat("\nReading mcsm combined data file: ", infile_params)
pd_df = plotting_data(my_df) 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() my_df_u = pd_df[[1]] # this forms one of the input for combining_dfs_plotting()
#-------------------------------- #--------------------------------
# call: combining_dfs_plotting() # call: combining_dfs_plotting()
#-------------------------------- #--------------------------------
#if (!exists("infile_metadata") && exists("gene")){ #if (!exists("infile_metadata") && exists("gene")){
if (!is.character(infile_params) && 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 in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
infile_metadata = paste0(outdir, "/", in_filename_metadata) infile_metadata = paste0(outdir, "/", in_filename_metadata)
cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n") cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
@ -91,12 +92,7 @@ all_plot_dfs = combining_dfs_plotting(my_df_u
, lig_dist_colname = 'ligand_distance' , lig_dist_colname = 'ligand_distance'
, lig_dist_cutoff = 10) , lig_dist_cutoff = 10)
#merged_df2 = all_plot_dfs[[1]]
merged_df3 = all_plot_dfs[[2]] 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 # output