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added additional check in combining_df_plotting.R to account for check when generating merged_df2 as muts NOT present in mcsm can create trouble, so fixed that and ran it successfully for alr and katg

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Tanushree Tunstall 2022-01-18 17:36:54 +00:00
parent 8f8a9db92c
commit e2cdee2d08
4 changed files with 62 additions and 30 deletions
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14
scripts/functions/tests/test_combining_dfs_plotting.R
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@ -36,8 +36,9 @@ source("combining_dfs_plotting.R")
#---------------------
# call: import_dirs()
#---------------------
gene = 'gid'
drug = 'streptomycin'
#gene = 'gid'
#drug = 'streptomycin'
source("/home/tanu/git/LSHTM_analysis/config/alr.R")
import_dirs(drug_name = drug, gene_name = gene)
@ -59,8 +60,9 @@ mcsm_comb_data = read.csv(infile_params, header = T)
# call function: plotting_data()
#-------------------------------
pd_df = plotting_data(df = mcsm_comb_data
, ligand_dist_colname = 'ligand_distance'
, lig_dist_cutoff = 10
, lig_dist_colname = LigDist_colname
, lig_dist_cutoff = LigDist_cutoff)
my_df_u = pd_df[[2]]
#======================================
@ -84,8 +86,8 @@ gene_metadata <- read.csv(infile_metadata
#-----------------------------------------
all_plot_dfs = combining_dfs_plotting(my_df_u
, gene_metadata
, lig_dist_colname = 'ligand_distance'
, lig_dist_cutoff = 10)
, lig_dist_colname = LigDist_colname
, lig_dist_cutoff = LigDist_cutoff)
merged_df2 = all_plot_dfs[[1]]
merged_df3 = all_plot_dfs[[2]]