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SNP -> SAV for thesis plots

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This commit is contained in:
Tanushree Tunstall 2023-02-19 17:43:22 +00:00
parent 777d3765cf
commit db7e2912e1
31 changed files with 145 additions and 145 deletions
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14
scripts/functions/position_count_bp.R
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@ -1,7 +1,7 @@
#!/usr/bin/env Rscript
#########################################################
# TASK: function for barplot showing no. of sites with nsSNP
# TASK: function for barplot showing no. of sites with SAV
# count
#########################################################
# load libraries and functions
@ -11,7 +11,7 @@ library(dplyr)
theme_set(theme_grey())
#=================================================================
# site_snp_count_bp(): barplots for no. of sites and nsSNP count
# site_snp_count_bp(): barplots for no. of sites and SAV count
# input args
## df containing data to plot
## df column name containing site/position numbers
@ -31,7 +31,7 @@ site_snp_count_bp <- function (plotdf,
axis_label_size = 10,#22
subtitle_size = 10,#20
geom_ls = 10,
xaxis_title = "Number of nsSNPs",
xaxis_title = "Number of SAVs",
yaxis_title = "Number of Sites",
title_colour = "chocolate4",
subtitle_text = NULL,
@ -82,7 +82,7 @@ site_snp_count_bp <- function (plotdf,
# sanity check
if(tot_muts == nrow(plotdf)){
cat("\nPASS: total number of mutations match"
, "\nTotal no. of nsSNPs:", tot_muts)
, "\nTotal no. of SAVs:", tot_muts)
} else{
cat("\nWARNING: total no. of muts = ", tot_muts
, "\nExpected = ", nrow(plotdf))
@ -106,13 +106,13 @@ site_snp_count_bp <- function (plotdf,
, table(snpsBYpos_df$snpsBYpos)
, "\n")
# calculating total no. of sites associated with nsSNPs
# calculating total no. of sites associated with SAVs
tot_sites = sum(table(snpsBYpos_df$snpsBYpos))
# sanity check
if(tot_sites == length(unique(plotdf$position))){
cat("\nPASS: total number of mutation sites match"
, "\nTotal no. of sites with nsSNPs:", tot_sites)
, "\nTotal no. of sites with SAVs:", tot_sites)
} else{
cat("WARNING: total no. of sites = ", tot_sites
, "\nExpected = ", length(unique(plotdf$position)))
@ -121,7 +121,7 @@ site_snp_count_bp <- function (plotdf,
# FIXME: should really be legend title
# but atm being using as plot title
#my_leg_title
bp_plot_title = paste0("Total nsSNPs: ", tot_muts
bp_plot_title = paste0("Total SAVs: ", tot_muts
, "\nTotal sites: ", tot_sites)
#-------------