moved plotting_func to functions and replaced 3 basic_barplots scripts with 1
This commit is contained in:
parent
5c018e23be
commit
dccdfe9742
9 changed files with 287 additions and 237 deletions
182
scripts/plotting/basic_barplots.R
Executable file
182
scripts/plotting/basic_barplots.R
Executable file
|
|
@ -0,0 +1,182 @@
|
|||
#!/usr/bin/env Rscript
|
||||
#########################################################
|
||||
# TASK: Barplots for mCSM DUET, ligand affinity, and foldX
|
||||
# basic barplots with count of mutations
|
||||
# basic barplots with frequency of count of mutations
|
||||
#########################################################
|
||||
# working dir
|
||||
setwd("~/git/LSHTM_analysis/scripts/plotting")
|
||||
getwd()
|
||||
|
||||
|
||||
# load libraries
|
||||
#source("Header_TT.R")
|
||||
library(ggplot2)
|
||||
library(data.table)
|
||||
library(dplyr)
|
||||
require("getopt", quietly = TRUE) # cmd parse arguments
|
||||
|
||||
# load functions
|
||||
source("functions/plotting_globals.R")
|
||||
source("functions/plotting_data.R")
|
||||
source("functions/stability_count_bp.R")
|
||||
source("functions/position_count_bp.R")
|
||||
#############################################################
|
||||
# command line args
|
||||
#********************
|
||||
# !!!FUTURE TODO!!!
|
||||
# Can pass additional params of output/plot dir by user.
|
||||
# Not strictly required for my workflow since it is optimised
|
||||
# to have a streamlined input/output flow without filename worries.
|
||||
#********************
|
||||
spec = matrix(c(
|
||||
"drug" ,"d", 1, "character",
|
||||
"gene" ,"g", 1, "character",
|
||||
"data" ,"f", 2, "character"
|
||||
), byrow = TRUE, ncol = 4)
|
||||
|
||||
opt = getopt(spec)
|
||||
|
||||
#FIXME: detect if script running from cmd, then set these
|
||||
drug = opt$drug
|
||||
gene = opt$gene
|
||||
infile = opt$data
|
||||
|
||||
# hardcoding when not using cmd
|
||||
#drug = "streptomycin"
|
||||
#gene = "gid"
|
||||
|
||||
if(is.null(drug)|is.null(gene)) {
|
||||
stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
|
||||
}
|
||||
#########################################################
|
||||
# call functions with relevant args
|
||||
#***********************************
|
||||
# import_dirs(): returns
|
||||
# datadir
|
||||
# indir
|
||||
# outdir
|
||||
# plotdir
|
||||
# dr_muts_col
|
||||
# other_muts_col
|
||||
# resistance_col
|
||||
#***********************************
|
||||
import_dirs(drug, gene)
|
||||
#***********************************
|
||||
# plotting_data(): returns
|
||||
# my_df
|
||||
# my_df_u
|
||||
# my_df_u_lig
|
||||
# dup_muts
|
||||
#***********************************
|
||||
#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
|
||||
#infile = ""
|
||||
|
||||
#if (!exists("infile") && exists("gene")){
|
||||
if (!is.character(infile) && exists("gene")){
|
||||
#in_filename_params = paste0(tolower(gene), "_all_params.csv")
|
||||
in_filename_params = paste0(tolower(gene), "_comb_stab_struc_params.csv") # part combined for gid
|
||||
infile = paste0(outdir, "/", in_filename_params)
|
||||
cat("\nInput file not specified, assuming filename: ", infile, "\n")
|
||||
}
|
||||
|
||||
# Get the DFs out of plotting_data()
|
||||
pd_df = plotting_data(infile)
|
||||
my_df = pd_df[[1]]
|
||||
my_df_u = pd_df[[2]]
|
||||
my_df_u_lig = pd_df[[3]]
|
||||
dup_muts = pd_df[[4]]
|
||||
|
||||
cat(paste0("Directories imported:"
|
||||
, "\ndatadir:", datadir
|
||||
, "\nindir:", indir
|
||||
, "\noutdir:", outdir
|
||||
, "\nplotdir:", plotdir))
|
||||
|
||||
cat(paste0("\nVariables imported:"
|
||||
, "\ndrug:", drug
|
||||
, "\ngene:", gene
|
||||
, "\n"))
|
||||
#=======================================================================
|
||||
#=======
|
||||
# output
|
||||
#=======
|
||||
cat("plots will output to:", plotdir)
|
||||
#=======================================================================
|
||||
# begin plots
|
||||
|
||||
# ------------------------------
|
||||
# barplot for mscm stability
|
||||
# ------------------------------
|
||||
basic_bp_duet = paste0(tolower(gene), "_basic_barplot_PS.svg")
|
||||
plot_basic_bp_duet = paste0(plotdir,"/", basic_bp_duet)
|
||||
|
||||
svg(plot_basic_bp_duet)
|
||||
print(paste0("plot filename:", basic_bp_duet))
|
||||
|
||||
# function only
|
||||
stability_count_bp(plotdf = my_df_u
|
||||
, df_colname = "duet_outcome"
|
||||
, leg_title = "DUET outcome")
|
||||
|
||||
dev.off()
|
||||
|
||||
# ------------------------------
|
||||
# barplot for ligand affinity
|
||||
# ------------------------------
|
||||
basic_bp_ligand = paste0(tolower(gene), "_basic_barplot_LIG.svg")
|
||||
plot_basic_bp_ligand = paste0(plotdir, "/", basic_bp_ligand)
|
||||
|
||||
svg(plot_basic_bp_ligand)
|
||||
print(paste0("plot filename:", basic_bp_ligand))
|
||||
|
||||
# function only
|
||||
stability_count_bp(plotdf = my_df_u_lig
|
||||
, df_colname = "ligand_outcome"
|
||||
, leg_title = "Ligand outcome"
|
||||
, bp_plot_title = "Sites < 10 Ang of ligand")
|
||||
|
||||
dev.off()
|
||||
# ------------------------------
|
||||
# barplot for foldX
|
||||
# ------------------------------
|
||||
basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
|
||||
plot_basic_bp_foldx = paste0(plotdir,"/", basic_bp_foldx)
|
||||
|
||||
svg(plot_basic_bp_foldx)
|
||||
print(paste0("plot filename:", plot_basic_bp_foldx))
|
||||
|
||||
stability_count_bp(plotdf = my_df_u
|
||||
, df_colname = "foldx_outcome"
|
||||
, leg_title = "FoldX outcome")
|
||||
dev.off()
|
||||
#===============================================================
|
||||
# ------------------------------
|
||||
# barplot for nssnp site count: all
|
||||
# ------------------------------
|
||||
pos_count_duet = paste0(tolower(gene), "_position_count_PS.svg")
|
||||
plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
|
||||
|
||||
svg(plot_pos_count_duet)
|
||||
print(paste0("plot filename:", plot_pos_count_duet))
|
||||
|
||||
# function only
|
||||
site_snp_count_bp(plotdf = my_df_u
|
||||
, df_colname = "position")
|
||||
|
||||
dev.off()
|
||||
# ------------------------------
|
||||
# barplot for nssnp site count: within 10 Ang
|
||||
# ------------------------------
|
||||
pos_count_ligand = paste0(tolower(gene), "_position_count_LIG.svg")
|
||||
plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
|
||||
|
||||
svg(plot_pos_count_ligand)
|
||||
print(paste0("plot filename:", plot_pos_count_ligand))
|
||||
|
||||
# function only
|
||||
site_snp_count_bp(plotdf = my_df_u_lig
|
||||
, df_colname = "position")
|
||||
|
||||
dev.off()
|
||||
#===============================================================
|
||||
|
|
@ -21,8 +21,10 @@ library(dplyr)
|
|||
require("getopt", quietly = TRUE) # cmd parse arguments
|
||||
|
||||
# load functions
|
||||
source("plotting_globals.R")
|
||||
source("plotting_data.R")
|
||||
source("functions/plotting_globals.R")
|
||||
source("functions/plotting_data.R")
|
||||
source("functions/stability_count_bp.R")
|
||||
source("functions/position_count_bp.R")
|
||||
#########################################################
|
||||
# command line args
|
||||
#********************
|
||||
|
|
@ -117,17 +119,7 @@ plot_basic_bp_ligand = paste0(plotdir,"/", basic_bp_ligand)
|
|||
# plot 2
|
||||
pos_count_ligand = paste0(tolower(gene), "_position_count_LIG.svg")
|
||||
plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
|
||||
|
||||
#=======================================================================
|
||||
#================
|
||||
# Data for plots
|
||||
#================
|
||||
# REASSIGNMENT as necessary
|
||||
df = my_df_u_lig
|
||||
|
||||
# sanity checks
|
||||
str(df)
|
||||
#=====================================================================
|
||||
#****************
|
||||
# Plot 1: Count of stabilising and destabilsing muts
|
||||
#****************
|
||||
|
|
@ -135,9 +127,6 @@ str(df)
|
|||
svg(plot_basic_bp_ligand)
|
||||
print(paste0("plot1 filename:", basic_bp_ligand))
|
||||
|
||||
#--------------
|
||||
# start plot 1: call function
|
||||
#--------------
|
||||
stability_count_bp(plotdf = my_df_u_lig
|
||||
, df_colname = "ligand_outcome"
|
||||
, leg_title = "Ligand outcome")
|
||||
|
|
@ -148,84 +137,12 @@ table(my_df_u_lig$ligand_outcome)
|
|||
#****************
|
||||
# Plot 2: frequency of positions
|
||||
#****************
|
||||
df_ncols = ncol(df)
|
||||
df_nrows = nrow(df)
|
||||
|
||||
cat(paste0("original df dimensions:"
|
||||
, "\nNo. of rows:", df_nrows
|
||||
, "\nNo. of cols:", df_ncols
|
||||
, "\nNow adding column: frequency of mutational positions"))
|
||||
|
||||
#setDT(df)[, .(pos_count := .N), by = .(position)]
|
||||
setDT(df)[, pos_count := .N, by = .(position)]
|
||||
|
||||
rm(df_nrows, df_ncols)
|
||||
|
||||
df_nrows = nrow(df)
|
||||
df_ncols = ncol(df)
|
||||
|
||||
cat(paste0("revised df dimensions:"
|
||||
, "\nNo. of rows:", df_nrows
|
||||
, "\nNo. of cols:", df_ncols))
|
||||
|
||||
# this is cummulative
|
||||
table(df$pos_count)
|
||||
|
||||
# use group by on this
|
||||
snpsBYpos_df <- df %>%
|
||||
group_by(position) %>%
|
||||
summarize(snpsBYpos = mean(pos_count))
|
||||
|
||||
table(snpsBYpos_df$snpsBYpos)
|
||||
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
# FIXME, get this mutation_info, perhaLIG useful!
|
||||
foo = select(df, mutationinformation
|
||||
, wild_pos
|
||||
, wild_type
|
||||
, mutant_type
|
||||
#, mutation_info # comes from meta data, notused yet
|
||||
, position
|
||||
, pos_count)
|
||||
|
||||
#write.csv(foo, "/pos_count_freq.csv")
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
|
||||
#--------------
|
||||
# start plot 2
|
||||
#--------------
|
||||
#svg("position_count_LIG.svg")
|
||||
svg(plot_pos_count_ligand)
|
||||
print(paste0("plot filename:", plot_pos_count_ligand))
|
||||
|
||||
my_ats = 25 # axis text size
|
||||
my_als = 22 # axis label size
|
||||
site_snp_count_bp(plotdf = my_df_u
|
||||
, df_colname = "position")
|
||||
|
||||
# to make x axis display all positions
|
||||
# not sure if to use with sort or directly
|
||||
my_x = sort(unique(snpsBYpos_df$snpsBYpos))
|
||||
|
||||
g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
|
||||
OutPlot_lig_pos_count = g + geom_bar(aes (alpha = 0.5)
|
||||
, show.legend = FALSE) +
|
||||
scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
|
||||
#scale_x_continuous(breaks = my_x) +
|
||||
geom_label(stat = "count", aes(label = ..count..)
|
||||
, color = "black"
|
||||
, size = 10) +
|
||||
theme(axis.text.x = element_text(size = my_ats
|
||||
, angle = 0)
|
||||
, axis.text.y = element_text(size = my_ats
|
||||
, angle = 0
|
||||
, hjust = 1)
|
||||
, axis.title.x = element_text(size = my_als)
|
||||
, axis.title.y = element_text(size = my_als)
|
||||
, plot.title = element_blank()) +
|
||||
|
||||
labs(x = "Number of nsSNPs"
|
||||
, y = "Number of Sites")
|
||||
|
||||
print(OutPlot_lig_pos_count)
|
||||
dev.off()
|
||||
########################################################################
|
||||
# end of LIG barplots
|
||||
|
|
|
|||
|
|
@ -21,9 +21,10 @@ library(dplyr)
|
|||
require("getopt", quietly = TRUE) # cmd parse arguments
|
||||
|
||||
# load functions
|
||||
source("plotting_globals.R")
|
||||
source("plotting_data.R")
|
||||
source("functions/plotting_globals.R")
|
||||
source("functions/plotting_data.R")
|
||||
source("functions/stability_count_bp.R")
|
||||
source("functions/position_count_bp.R")
|
||||
#########################################################
|
||||
# command line args
|
||||
#********************
|
||||
|
|
@ -118,15 +119,6 @@ plot_basic_bp_duet = paste0(plotdir,"/", basic_bp_duet)
|
|||
pos_count_duet = paste0(tolower(gene), "_position_count_PS.svg")
|
||||
plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
|
||||
|
||||
#=======================================================================
|
||||
#================
|
||||
# Data for plots
|
||||
#================
|
||||
# REASSIGNMENT as necessary
|
||||
df = my_df_u
|
||||
|
||||
# sanity checks
|
||||
str(df)
|
||||
#=======================================================================
|
||||
#****************
|
||||
# Plot 1: Count of stabilising and destabilsing muts
|
||||
|
|
@ -134,9 +126,7 @@ str(df)
|
|||
svg(plot_basic_bp_duet)
|
||||
print(paste0("plot1 filename:", basic_bp_duet))
|
||||
|
||||
#--------------
|
||||
# start plot 1: call function
|
||||
#--------------
|
||||
|
||||
stability_count_bp(plotdf = my_df_u
|
||||
, df_colname = "duet_outcome"
|
||||
, leg_title = "DUET outcome")
|
||||
|
|
@ -147,82 +137,12 @@ table(my_df_u$duet_outcome)
|
|||
#****************
|
||||
# Plot 2: frequency of positions
|
||||
#****************
|
||||
df_ncols = ncol(df)
|
||||
df_nrows = nrow(df)
|
||||
|
||||
cat(paste0("original df dimensions:"
|
||||
, "\nNo. of rows:", df_nrows
|
||||
, "\nNo. of cols:", df_ncols
|
||||
, "\nNow adding column: frequency of mutational positions"))
|
||||
|
||||
#setDT(df)[, .(pos_count := .N), by = .(position)]
|
||||
setDT(df)[, pos_count := .N, by = .(position)]
|
||||
|
||||
rm(df_nrows, df_ncols)
|
||||
|
||||
df_nrows = nrow(df)
|
||||
df_ncols = ncol(df)
|
||||
|
||||
cat(paste0("revised df dimensions:"
|
||||
, "\nNo. of rows:", df_nrows
|
||||
, "\nNo. of cols:", df_ncols))
|
||||
|
||||
# this is cummulative
|
||||
table(df$pos_count)
|
||||
|
||||
# use group by on this
|
||||
snpsBYpos_df <- df %>%
|
||||
group_by(position) %>%
|
||||
summarize(snpsBYpos = mean(pos_count))
|
||||
|
||||
table(snpsBYpos_df$snpsBYpos)
|
||||
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
# FIXME, get this mutation_info, perhaps useful!
|
||||
foo = select(df, mutationinformation
|
||||
, wild_pos
|
||||
, wild_type
|
||||
, mutant_type
|
||||
#, mutation_info # comes from meta data, notused yet
|
||||
, position
|
||||
, pos_count)
|
||||
|
||||
#write.csv(foo, "/pos_count_freq.csv")
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
|
||||
#--------------
|
||||
# start plot 2
|
||||
#--------------
|
||||
svg(plot_pos_count_duet)
|
||||
print(paste0("plot filename:", plot_pos_count_duet))
|
||||
my_ats = 25 # axis text size
|
||||
my_als = 22 # axis label size
|
||||
|
||||
# to make x axis display all positions
|
||||
# not sure if to use with sort or directly
|
||||
my_x = sort(unique(snpsBYpos_df$snpsBYpos))
|
||||
|
||||
g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
|
||||
OutPlot_pos_count = g + geom_bar(aes (alpha = 0.5)
|
||||
, show.legend = FALSE) +
|
||||
scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
|
||||
#scale_x_continuous(breaks = my_x) +
|
||||
geom_label(stat = "count", aes(label = ..count..)
|
||||
, color = "black"
|
||||
, size = 10) +
|
||||
theme(axis.text.x = element_text(size = my_ats
|
||||
, angle = 0)
|
||||
, axis.text.y = element_text(size = my_ats
|
||||
, angle = 0
|
||||
, hjust = 1)
|
||||
, axis.title.x = element_text(size = my_als)
|
||||
, axis.title.y = element_text(size = my_als)
|
||||
, plot.title = element_blank()) +
|
||||
|
||||
labs(x = "Number of nsSNPs"
|
||||
, y = "Number of Sites")
|
||||
|
||||
print(OutPlot_pos_count)
|
||||
# function only
|
||||
site_snp_count_bp(plotdf = my_df_u
|
||||
, df_colname = "position")
|
||||
|
||||
dev.off()
|
||||
########################################################################
|
||||
|
|
|
|||
|
|
@ -54,26 +54,23 @@ if(is.null(drug)|is.null(gene)) {
|
|||
}
|
||||
#########################################################
|
||||
# call functions with relevant args
|
||||
|
||||
#------------------------------------------
|
||||
# import_dirs()
|
||||
# should return the follwoing variables:
|
||||
# datadir
|
||||
# indir
|
||||
# outdir
|
||||
# plotdir
|
||||
# dr_muts_col
|
||||
# other_muts_col
|
||||
# resistance_col
|
||||
# import_dirs(); returns
|
||||
# datadir
|
||||
# indir
|
||||
# outdir
|
||||
# plotdir
|
||||
# dr_muts_col
|
||||
# other_muts_col
|
||||
# resistance_col
|
||||
#--------------------------------------------
|
||||
import_dirs(drug, gene)
|
||||
#---------------------------------------------
|
||||
# plotting_data()
|
||||
# should return the following dfs:
|
||||
# my_df
|
||||
# my_df_u
|
||||
# my_df_u_lig
|
||||
# dup_muts
|
||||
# plotting_data(): returns
|
||||
# my_df
|
||||
# my_df_u
|
||||
# my_df_u_lig
|
||||
# dup_muts
|
||||
#----------------------------------------------
|
||||
#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
|
||||
#infile = ""
|
||||
|
|
@ -107,32 +104,20 @@ cat(paste0("Directories imported:"
|
|||
#, "\ngene_match:", gene_match
|
||||
#, "\nLength of upos:", length(upos)
|
||||
#, "\nAngstrom symbol:", angstroms_symbol))
|
||||
#======================================================================
|
||||
|
||||
#=======
|
||||
# output
|
||||
# output filenames
|
||||
#=======
|
||||
# plot 1
|
||||
|
||||
basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
|
||||
plot_basic_bp_foldx = paste0(plotdir,"/", basic_bp_foldx)
|
||||
#=======================================================================
|
||||
#================
|
||||
# Data for plots
|
||||
#================
|
||||
# REASSIGNMENT as necessary
|
||||
df = my_df_u
|
||||
|
||||
# sanity checks
|
||||
str(df)
|
||||
#=======================================================================
|
||||
#****************
|
||||
# Plot 1: Count of stabilising and destabilsing muts
|
||||
#****************
|
||||
svg(plot_basic_bp_foldx)
|
||||
print(paste0("plot1 filename:", plot_basic_bp_foldx))
|
||||
|
||||
#--------------
|
||||
# start plot 1: call function
|
||||
#--------------
|
||||
stability_count_bp(plotdf = my_df_u
|
||||
, df_colname = "foldx_outcome"
|
||||
, leg_title = "FoldX outcome")
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ site_snp_count_bp <- function (plotdf
|
|||
, df_colname = "position"
|
||||
#, bp_plot_title = ""
|
||||
#, leg_title = "Legend title"
|
||||
#, leg_text_size = 20
|
||||
, leg_text_size = 20
|
||||
, axis_text_size = 25
|
||||
, axis_label_size = 22
|
||||
, xaxis_title = "Number of nsSNPs"
|
||||
|
|
@ -111,7 +111,7 @@ site_snp_count_bp <- function (plotdf
|
|||
#, legend.position = c(0.73,0.8)
|
||||
#, legend.text = element_text(size = leg_text_size)
|
||||
#, legend.title = element_text(size = axis_label_size)
|
||||
, plot.title = element_text(size = axis_label_size)) +
|
||||
, plot.title = element_text(size = leg_text_size)) +
|
||||
|
||||
labs(title = bp_plot_title
|
||||
, x = xaxis_title
|
||||
|
|
|
|||
|
|
@ -1,9 +1,10 @@
|
|||
setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
|
||||
getwd()
|
||||
|
||||
# =================
|
||||
# Test function
|
||||
# ==================
|
||||
#############################################################
|
||||
#===========================================
|
||||
# load functions, data, dirs, hardocded vars
|
||||
# that will be used in testing the functions
|
||||
#===========================================
|
||||
source("../plotting_data.R")
|
||||
infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
|
||||
pd_df = plotting_data(infile)
|
||||
|
|
@ -12,30 +13,91 @@ my_df_u = pd_df[[2]]
|
|||
my_df_u_lig = pd_df[[3]]
|
||||
dup_muts = pd_df[[4]]
|
||||
|
||||
source("../plotting_globals.R")
|
||||
drug = "streptomycin"
|
||||
gene = "gid"
|
||||
|
||||
import_dirs(drug, gene)
|
||||
|
||||
#=====================
|
||||
# functions to test
|
||||
#=====================
|
||||
source("stability_count_bp.R")
|
||||
source("position_count_bp.R")
|
||||
|
||||
##################################################################
|
||||
# ------------------------------
|
||||
# barplot for mscm stability
|
||||
# ------------------------------
|
||||
basic_bp_duet = paste0(tolower(gene), "_basic_barplot_PS.svg")
|
||||
plot_basic_bp_duet = paste0(plotdir,"/", basic_bp_duet)
|
||||
|
||||
svg(plot_basic_bp_duet)
|
||||
print(paste0("plot filename:", basic_bp_duet))
|
||||
|
||||
# function only
|
||||
stability_count_bp(plotdf = my_df_u
|
||||
, df_colname = "duet_outcome"
|
||||
, leg_title = "DUET outcome")
|
||||
|
||||
dev.off()
|
||||
|
||||
# ------------------------------
|
||||
# barplot for ligand affinity
|
||||
# ------------------------------
|
||||
basic_bp_ligand = paste0(tolower(gene), "_basic_barplot_LIG.svg")
|
||||
plot_basic_bp_ligand = paste0(plotdir, "/", basic_bp_ligand)
|
||||
|
||||
svg(plot_basic_bp_ligand)
|
||||
print(paste0("plot filename:", basic_bp_ligand))
|
||||
|
||||
# function only
|
||||
stability_count_bp(plotdf = my_df_u_lig
|
||||
, df_colname = "ligand_outcome"
|
||||
, leg_title = "Ligand outcome"
|
||||
, bp_plot_title = "Sites < 10 Ang of ligand"
|
||||
)
|
||||
, bp_plot_title = "Sites < 10 Ang of ligand")
|
||||
|
||||
dev.off()
|
||||
# ------------------------------
|
||||
# barplot for foldX
|
||||
# ------------------------------
|
||||
basic_bp_foldx = paste0(tolower(gene), "_basic_barplot_foldx.svg")
|
||||
plot_basic_bp_foldx = paste0(plotdir,"/", basic_bp_foldx)
|
||||
|
||||
svg(plot_basic_bp_foldx)
|
||||
print(paste0("plot filename:", plot_basic_bp_foldx))
|
||||
|
||||
stability_count_bp(plotdf = my_df_u
|
||||
, df_colname = "foldx_outcome"
|
||||
, leg_title = "FoldX outcome")
|
||||
dev.off()
|
||||
#===============================================================
|
||||
# ------------------------------
|
||||
# barplot for nssnp site count: all
|
||||
# ------------------------------
|
||||
pos_count_duet = paste0(tolower(gene), "_position_count_PS.svg")
|
||||
plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
|
||||
|
||||
svg(plot_pos_count_duet)
|
||||
print(paste0("plot filename:", plot_pos_count_duet))
|
||||
|
||||
# function only
|
||||
site_snp_count_bp(plotdf = my_df_u
|
||||
, df_colname = "position")
|
||||
|
||||
dev.off()
|
||||
# ------------------------------
|
||||
# barplot for nssnp site count: within 10 Ang
|
||||
# ------------------------------
|
||||
pos_count_ligand = paste0(tolower(gene), "_position_count_LIG.svg")
|
||||
plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
|
||||
|
||||
svg(plot_pos_count_ligand)
|
||||
print(paste0("plot filename:", plot_pos_count_ligand))
|
||||
|
||||
# function only
|
||||
site_snp_count_bp(plotdf = my_df_u_lig
|
||||
, df_colname = "position")
|
||||
|
||||
dev.off()
|
||||
#===============================================================
|
||||
|
|
@ -1,12 +1,16 @@
|
|||
#========
|
||||
# basic_barplots_PS.R:
|
||||
# basic_barplot.R:
|
||||
#========
|
||||
./basic_barplots_PS.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv
|
||||
./basic_barplots.R -d streptomycin -g gid -f /home/tanu/gid_test_file.csv
|
||||
|
||||
sources:
|
||||
## plotting_globals.R (previously dir.R)
|
||||
## plotting_data.R
|
||||
## position_count_bp.R
|
||||
## stability_count_bp.R
|
||||
|
||||
outputs:
|
||||
#5 svgs in the plotdir
|
||||
|
||||
# TODO
|
||||
Delete: dirs.R
|
||||
|
|
@ -17,23 +21,3 @@ resolving_ambiguous_muts.R:source("dirs.R")
|
|||
|
||||
#=======================================================================
|
||||
|
||||
#========
|
||||
# basic_barplots_foldx.R:
|
||||
#========
|
||||
./basic_barplots_foldx.R -d streptomycin -g gid
|
||||
# picks default file name, or you can specify by the -f flag
|
||||
|
||||
sources:
|
||||
## plotting_globals.R (previously dir.R)
|
||||
## plotting_data.R
|
||||
|
||||
#========
|
||||
# basic_barplots_LIG.R:
|
||||
#========
|
||||
./basic_barplots_LIG.R -d streptomycin -g gid
|
||||
# picks default file name, or you can specify by the -f flag
|
||||
|
||||
sources:
|
||||
## plotting_globals.R (previously dir.R)
|
||||
## plotting_data.R
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue