From 2f7f40efb1df8f803b610cd46734163a8081ff44 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Wed, 26 Jan 2022 15:22:13 +0000 Subject: [PATCH] added a few tweaks to check logoplots --- scripts/functions/logoP_msa.R | 7 +++---- scripts/functions/tests/test_logo_plots.R | 10 +++++----- 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/scripts/functions/logoP_msa.R b/scripts/functions/logoP_msa.R index 7c1f7da..a3ab3f9 100644 --- a/scripts/functions/logoP_msa.R +++ b/scripts/functions/logoP_msa.R @@ -57,7 +57,7 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector cat("\nY-axis lower limit:", ylim_low) 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) y_rup = seq(0, ylim_up, by = 2); y_rup }else{ @@ -185,9 +185,7 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector , "\nFiltering positions as specified..." , "\nNo. of positions in plot:", length(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 #------------------ @@ -195,6 +193,7 @@ LogoPlotMSA <- function(msaSeq_mut # chr vector plot_mut_edM = data_logo_mut[, i_extract] plot_wt_edM = data_logo_wt[, i_extract] + } if (logo_type%in%c("bits_raw", "probability_raw")){ diff --git a/scripts/functions/tests/test_logo_plots.R b/scripts/functions/tests/test_logo_plots.R index 581f803..94d42b4 100644 --- a/scripts/functions/tests/test_logo_plots.R +++ b/scripts/functions/tests/test_logo_plots.R @@ -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/embb.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/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 , 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") , bg_prob = NULL , 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_filtered = 0.05 , y_axis_offset = 0.05 - #, y_breaks + #, y_breaks = c(0, 2, 4, 6, 8, 10, 12) , x_lab_mut = "nsSNP-position" #, y_lab_mut , x_ats = 10