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renamed logoP_msa.R --> logoP_msa_raw.R

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Tanushree Tunstall 2022-01-26 11:03:45 +00:00
parent 6a9f4a0cab
commit 3bc5dcbad3
4 changed files with 316 additions and 267 deletions
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100
scripts/functions/tests/test_logo_plots.R
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@ -1,12 +1,12 @@
#source("~/git/LSHTM_analysis/config/gid.R")
source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/alr.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
# mainly OR
@ -61,7 +61,6 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
# , leg_ts = 14 # leg text size
# , leg_tts = 16 # leg title size
# )
#
########################################
# Logo plot MSA
@ -71,31 +70,84 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
# specify {plot_positions}
# To plot entire MSA, simply don't specify {plot_positions}
# script: logoP_msa.R
# TODO perhaps: ED logo from Logolas
# TODO: Add scaled data option
########################################
LogoPlotMSA(msaSeq_mut = msa_seq
, msaSeq_wt = wt_seq
, msa_method = 'bits' # or probability
, my_logo_col = "taylor"
, plot_positions = active_aa_pos
, x_lab = "nsSNP position"
, y_lab = ""
, x_ats = 10 # text size
, x_tangle = 90 # text angle
, x_axis_offset = 0.05
, y_ats = 15
, y_tangle = 0
, x_tts = 13 # title size
, y_tts = 15
, leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
, leg_dir = "horizontal" #can be vertical or horizontal
, leg_ts = 16 # leg text size
, leg_tts = 16 # leg title size
)
# LogoPlotMSA(msaSeq_mut = msa_seq
# , msaSeq_wt = wt_seq
# # , use_pfm
# # , use_pfm_scaled
# # , use_ed
# , msa_method = 'bits' # or probability
# , my_logo_col = "taylor"
# , plot_positions = 1:15
# , x_lab = "nsSNP position"
# , y_lab = ""
# , x_ats = 10 # text size
# , x_tangle = 90 # text angle
# , x_axis_offset = 0.05
# , y_ats = 15
# , y_tangle = 0
# , x_tts = 13 # title size
# , y_tts = 15
# , leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
# , leg_dir = "horizontal" #can be vertical or horizontal
# , leg_ts = 16 # leg text size
# , leg_tts = 16 # leg title size
# )
########################################
# ED Logo plot MSA
# Mutant and wild-type
########################################
# library(Logolas)
# library(ggseqlogo)
# source("~/git/LSHTM_analysis/scripts/functions/my_logolas.R")
# source("~/git/LSHTM_analysis/scripts/functions/logoP_logolas.R")
#
# # data msa: mut
# my_data = read.csv("/home/tanu/git/Misc/practice_plots/pnca_msa_eg2.csv", header = F) #15 cols only
# msaSeq_mut = my_data$V1
# msa_seq = msaSeq_mut
#
# # data msa: wt
# gene = "pncA"
# drug = "pyrazinamide"
# indir = paste0("~/git/Data/", drug , "/input/")
#
# in_filename_fasta = paste0(tolower(gene), "2_f2.fasta")
# infile_fasta = paste0(indir, in_filename_fasta)
# cat("\nInput fasta file for WT: ", infile_fasta, "\n")
#
# msa2 = read.csv(infile_fasta, header = F)
# head(msa2)
# cat("\nLength of WT fasta:", nrow(msa2))
# wt_seq = msa2$V1
# head(wt_seq)
# msaSeq_wt = msa2$V1
# wt_seq = msaSeq_wt
#PlotLogolasMSA()
PlotLogolasMSA(msaSeq_mut = msa_seq
, msaSeq_wt = wt_seq
, logo_type = c("bits_pfm") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw") # can be "bits", "probability" or "custom"
, EDScore_type = c("log") # see if this relevant, or source function should have it!
, bg_prob = NULL
, my_logo_col = "taylor"
, plot_positions = c(1:15)
#, y_breaks
, x_lab_mut = "nsSNP-position"
#, y_lab_mut
, x_ats = 13 # text size
, x_tangle = 90 # text angle
, x_axis_offset = 0.05
, x_axis_offset_filtered = 0.05
, y_axis_offset = 0.05
, y_ats = 13
, y_tangle = 0
, x_tts = 13
, y_tts = 13
, leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
, leg_dir = "horizontal" #can be vertical or horizontal
, leg_ts = 16 # leg text size
, leg_tts = 16 # leg title size
)