63 lines
1.9 KiB
R
63 lines
1.9 KiB
R
#!/usr/bin/env Rscript
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library(ggplot2)
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library(tidyverse)
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library(data.table)
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setwd("~/git/LSHTM_analysis/scripts/functions/")
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getwd()
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#############################################################
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#===========================================
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# load functions, data, dirs, hardocded vars
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# that will be used in testing the functions
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#===========================================
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source("plotting_data.R")
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infile = "/home/tanu/git/Data/streptomycin/output/"
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pd_df = plotting_data(infile)
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my_df = pd_df[[1]]
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my_df_u = pd_df[[2]]
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my_df_u_lig = pd_df[[3]]
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dup_muts = pd_df[[4]]
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source("../plotting_globals.R")
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drug = "streptomycin"
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gene = "gid"
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import_dirs(drug, gene)
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#=====================
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# functions to test
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#=====================
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source("stability_count_bp.R")
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source("position_count_bp.R")
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#################################################################
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##############################################
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# read a sample file containing muts and prop
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###############################################
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df<- read.csv(file.choose())
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setDT(df)[, pos_count := .N, by = .(position)]
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foo = data.frame(df$position, df$pos_count)
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#snpsBYpos_df <- df %>%
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# group_by(position) %>%
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# summarize(snpsBYpos = mean(pos_count))
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# subset df without duplicates for position
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df2 = df[!duplicated(df$position)]
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##################################################################
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# ---------------------------------------
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# barplot for nssnps, coloured by aa prop
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# ---------------------------------------
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pos_colname = "position"
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aa_prop_colname = "mut_prop_water"
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aa_prop_colours = c("black", "blue")
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my_legname = "aa_prop: water"
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# call function
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aa_prop_bp(plotdf = df
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, position_colname = pos_colname
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, fill_colname = aa_prop_colname
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, fill_colours = aa_prop_cols
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, leg_name = my_legname)
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#===============================================================
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