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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/embb.R")
#---------------------------------------------------
# FIXME
# 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/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

6
scripts/gene_targets_names.txt
View file

@ -1,6 +1,6 @@
rpob rifampicin
embb ethambutol
alr cycloserine
gid streptomycin
katg isoniazid
pnca pyrazinamide
gid streptomycin
embb ethambutol
rpob rifampicin

2
scripts/plotting/logo_data_msa.R
View file

@ -39,7 +39,7 @@ head(msa_seq)
#================
#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)
cat("\nInput fasta file for WT: ", infile_fasta, "\n")