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just tested logo plot msa with embb after correcting the OMINOUS fasta file

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Tanushree Tunstall 2022-01-19 18:57:04 +00:00
parent 59eaf58747
commit b72ffb5d2c
3 changed files with 7 additions and 6 deletions
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5
scripts/functions/tests/test_logo_plots.R
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@ -1,5 +1,6 @@
source("~/git/LSHTM_analysis/config/gid.R") #source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/pnca.R") # YES #source("~/git/LSHTM_analysis/config/pnca.R") # YES
source("~/git/LSHTM_analysis/config/embb.R")
#--------------------------------------------------- #---------------------------------------------------
# FIXME # FIXME
# source("~/git/LSHTM_analysis/config/alr.R") # source("~/git/LSHTM_analysis/config/alr.R")
@ -7,7 +8,7 @@ source("~/git/LSHTM_analysis/config/gid.R")
# source("~/git/LSHTM_analysis/config/katg.R") # source("~/git/LSHTM_analysis/config/katg.R")
# source("~/git/LSHTM_analysis/config/rpob.R") # source("~/git/LSHTM_analysis/config/rpob.R")
#--------------------------------------------------- #---------------------------------------------------
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
# #
# ################################ # ################################
# # Logo plot with custom Y axis # # Logo plot with custom Y axis

6
scripts/gene_targets_names.txt
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@ -1,6 +1,6 @@
rpob rifampicin embb ethambutol
alr cycloserine alr cycloserine
gid streptomycin
katg isoniazid katg isoniazid
pnca pyrazinamide pnca pyrazinamide
gid streptomycin rpob rifampicin
embb ethambutol

2
scripts/plotting/logo_data_msa.R
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@ -39,7 +39,7 @@ head(msa_seq)
#================ #================
#in_filename_fasta = paste0(tolower(gene), ".1fasta") #in_filename_fasta = paste0(tolower(gene), ".1fasta")
in_filename_fasta = paste0(tolower(gene), "2.2fasta") # gid in_filename_fasta = paste0(tolower(gene), "2_f2.fasta") # gid
infile_fasta = paste0(indir, "/", in_filename_fasta) infile_fasta = paste0(indir, "/", in_filename_fasta)
cat("\nInput fasta file for WT: ", infile_fasta, "\n") cat("\nInput fasta file for WT: ", infile_fasta, "\n")