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added a few tweaks to check logoplots

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Tanushree Tunstall 2022-01-26 15:22:13 +00:00
parent 1b20f09075
commit 2f7f40efb1
2 changed files with 8 additions and 9 deletions
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5
scripts/functions/logoP_msa.R
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@ -57,7 +57,7 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector
cat("\nY-axis lower limit:", ylim_low) cat("\nY-axis lower limit:", ylim_low)
y_rlow = seq(0, ylim_low, length.out = 3); y_rlow y_rlow = seq(0, ylim_low, length.out = 3); y_rlow
ylim_up <- ceiling(max(data_logo_mut)) + 4; ylim_up ylim_up <- ceiling(max(data_logo_mut)) + 5; ylim_up
cat("\nY-axis upper limit:", ylim_up) cat("\nY-axis upper limit:", ylim_up)
y_rup = seq(0, ylim_up, by = 2); y_rup y_rup = seq(0, ylim_up, by = 2); y_rup
}else{ }else{
@ -185,8 +185,6 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector
, "\nFiltering positions as specified..." , "\nFiltering positions as specified..."
, "\nNo. of positions in plot:", length(plot_positions)) , "\nNo. of positions in plot:", length(plot_positions))
i_extract = plot_positions i_extract = plot_positions
#plot_mut_edM = data_logo_mut[, i_extract]
#plot_wt_edM = data_logo_wt[, i_extract]
#----------------- #-----------------
# PFM: mut + wt # PFM: mut + wt
@ -195,6 +193,7 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector
plot_mut_edM = data_logo_mut[, i_extract] plot_mut_edM = data_logo_mut[, i_extract]
plot_wt_edM = data_logo_wt[, i_extract] plot_wt_edM = data_logo_wt[, i_extract]
} }
if (logo_type%in%c("bits_raw", "probability_raw")){ if (logo_type%in%c("bits_raw", "probability_raw")){

10
scripts/functions/tests/test_logo_plots.R
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@ -1,8 +1,8 @@
#source("~/git/LSHTM_analysis/config/gid.R") 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/embb.R")
#source("~/git/LSHTM_analysis/config/katg.R") #source("~/git/LSHTM_analysis/config/katg.R")
source("~/git/LSHTM_analysis/config/alr.R") #source("~/git/LSHTM_analysis/config/alr.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")
@ -79,15 +79,15 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
LogoPlotMSA(msaSeq_mut = msa_seq LogoPlotMSA(msaSeq_mut = msa_seq
, msaSeq_wt = wt_seq , msaSeq_wt = wt_seq
, logo_type = c("bits_pfm") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw") , logo_type = c("EDLogo") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
, EDScore_type = c("log") , EDScore_type = c("log")
, bg_prob = NULL , bg_prob = NULL
, my_logo_col = "taylor" , my_logo_col = "taylor"
#, plot_positions = active_aa_pos #, plot_positions = c(5:10, 92, 195, 118:119)
, x_axis_offset = 0.02 , x_axis_offset = 0.02
, x_axis_offset_filtered = 0.05 , x_axis_offset_filtered = 0.05
, y_axis_offset = 0.05 , y_axis_offset = 0.05
#, y_breaks #, y_breaks = c(0, 2, 4, 6, 8, 10, 12)
, x_lab_mut = "nsSNP-position" , x_lab_mut = "nsSNP-position"
#, y_lab_mut #, y_lab_mut
, x_ats = 10 , x_ats = 10