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added functions dir for further tidying and tested this with ind scripts for stability

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This commit is contained in:
Tanushree Tunstall 2021-06-09 18:13:18 +01:00
parent 786eaabe1a
commit 4bee48f545
6 changed files with 108 additions and 107 deletions
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44
scripts/plotting/basic_barplots_LIG.R
View file

@ -99,9 +99,10 @@ cat(paste0("Directories imported:"
, "\noutdir:", outdir
, "\nplotdir:", plotdir))
cat(paste0("Variables imported:"
cat(paste0("\nVariables imported:"
, "\ndrug:", drug
, "\ngene:", gene))
, "\ngene:", gene
, "\n"))
#, "\ngene_match:", gene_match
#, "\nLength of upos:", length(upos)
#, "\nAngstrom symbol:", angstroms_symbol))
@ -130,46 +131,19 @@ str(df)
#****************
# Plot 1: Count of stabilising and destabilsing muts
#****************
#svg("basic_barplots_LIG.svg")
svg(plot_basic_bp_ligand)
print(paste0("plot1 filename:", basic_bp_ligand))
my_ats = 25 # axis text size
my_als = 22 # axis label size
theme_set(theme_grey())
#--------------
# start plot 1
# start plot 1: call function
#--------------
g = ggplot(df, aes(x = ligand_outcome))
OutPlot_lig_count = g + geom_bar(aes(fill = ligand_outcome)
, show.legend = TRUE) +
geom_label(stat = "count"
, aes(label = ..count..)
, color = "black"
, show.legend = FALSE
, size = 10) +
theme(axis.text.x = element_blank()
, axis.title.x = element_blank()
, axis.title.y = element_text(size=my_als)
, axis.text.y = element_text(size = my_ats)
, legend.position = c(0.73,0.8)
, legend.text = element_text(size=my_als-2)
, legend.title = element_text(size=my_als)
, plot.title = element_blank()) +
labs(title = ""
, y = "Number of nsSNPs"
#, fill="ligand_outcome"
) +
scale_fill_discrete(name = "Ligand Outcome"
, labels = c("Destabilising", "Stabilising"))
print(OutPlot_lig_count)
stability_count_bp(plotdf = my_df_u_lig
, df_colname = "ligand_outcome"
, leg_title = "Ligand outcome")
dev.off()
table(df$ligand_outcome)
table(my_df_u_lig$ligand_outcome)
#=======================================================================
#****************
# Plot 2: frequency of positions
@ -255,4 +229,4 @@ print(OutPlot_lig_pos_count)
dev.off()
########################################################################
# end of LIG barplots
########################################################################
########################################################################

45
scripts/plotting/basic_barplots_PS.R
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@ -23,6 +23,7 @@ require("getopt", quietly = TRUE) # cmd parse arguments
# load functions
source("plotting_globals.R")
source("plotting_data.R")
source("functions/stability_count_bp.R")
#########################################################
# command line args
#********************
@ -98,9 +99,10 @@ cat(paste0("Directories imported:"
, "\noutdir:", outdir
, "\nplotdir:", plotdir))
cat(paste0("Variables imported:"
cat(paste0("\nVariables imported:"
, "\ndrug:", drug
, "\ngene:", gene))
, "\ngene:", gene
, "\n))
#, "\ngene_match:", gene_match
#, "\nLength of upos:", length(upos)
#, "\nAngstrom symbol:", angstroms_symbol))
@ -129,45 +131,18 @@ str(df)
#****************
# Plot 1: Count of stabilising and destabilsing muts
#****************
svg(plot_basic_bp_duet)
print(paste0("plot1 filename:", basic_bp_duet))
my_ats = 25 # axis text size
my_als = 22 # axis label size
theme_set(theme_grey())
#--------------
# start plot 1
# start plot 1: call function
#--------------
g = ggplot(df, aes(x = duet_outcome))
OutPlot_count = g + geom_bar(aes(fill = duet_outcome)
, show.legend = TRUE) +
geom_label(stat = "count"
, aes(label = ..count..)
, color = "black"
, show.legend = FALSE
, size = 10) +
theme(axis.text.x = element_blank()
, axis.title.x = element_blank()
, axis.title.y = element_text(size=my_als)
, axis.text.y = element_text(size = my_ats)
, legend.position = c(0.73,0.8)
, legend.text = element_text(size=my_als-2)
, legend.title = element_text(size=my_als)
, plot.title = element_blank()) +
labs(title = ""
, y = "Number of nsSNPs"
#, fill="DUET Outcome"
) +
scale_fill_discrete(name = "DUET Outcome"
, labels = c("Destabilising", "Stabilising"))
print(OutPlot_count)
stability_count_bp(plotdf = my_df_u
, df_colname = "duet_outcome"
, leg_title = "DUET outcome")
dev.off()
table(df$duet_outcome)
table(my_df_u$duet_outcome)
#=======================================================================
#****************
# Plot 2: frequency of positions
@ -252,4 +227,4 @@ print(OutPlot_pos_count)
dev.off()
########################################################################
# end of PS barplots
########################################################################
########################################################################

45
scripts/plotting/basic_barplots_foldx.R
View file

@ -23,6 +23,7 @@ require("getopt", quietly = TRUE) # cmd parse arguments
# load functions
source("plotting_globals.R")
source("plotting_data.R")
source("functions/stability_count_bp.R")
#########################################################
# command line args
#********************
@ -99,9 +100,10 @@ cat(paste0("Directories imported:"
, "\noutdir:", outdir
, "\nplotdir:", plotdir))
cat(paste0("Variables imported:"
cat(paste0("\nVariables imported:"
, "\ndrug:", drug
, "\ngene:", gene))
, "\ngene:", gene
, "\n"))
#, "\ngene_match:", gene_match
#, "\nLength of upos:", length(upos)
#, "\nAngstrom symbol:", angstroms_symbol))
@ -125,45 +127,18 @@ str(df)
#****************
# Plot 1: Count of stabilising and destabilsing muts
#****************
svg(plot_basic_bp_foldx)
print(paste0("plot1 filename:", plot_basic_bp_foldx))
my_ats = 25 # axis text size
my_als = 22 # axis label size
theme_set(theme_grey())
#--------------
# start plot 1
# start plot 1: call function
#--------------
g = ggplot(df, aes(x = foldx_outcome))
foldx_outcome_count = g + geom_bar(aes(fill = foldx_outcome)
, show.legend = TRUE) +
geom_label(stat = "count"
, aes(label = ..count..)
, color = "black"
, show.legend = FALSE
, size = 10) +
theme(axis.text.x = element_blank()
, axis.title.x = element_blank()
, axis.title.y = element_text(size=my_als)
, axis.text.y = element_text(size = my_ats)
, legend.position = c(0.73,0.8)
, legend.text = element_text(size=my_als-2)
, legend.title = element_text(size=my_als)
, plot.title = element_blank()) +
labs(title = ""
, y = "Number of nsSNPs"
#, fill="FoldX Outcome"
) +
scale_fill_discrete(name = "FoldX Outcome"
, labels = c("Destabilising", "Stabilising"))
print(foldx_outcome_count)
stability_count_bp(plotdf = my_df_u
, df_colname = "foldx_outcome"
, leg_title = "FoldX outcome")
dev.off()
table(df$foldx_outcome)
table(my_df_u$foldx_outcome)
########################################################################
# end of foldx barplot
########################################################################
########################################################################

50
scripts/plotting/functions/stability_count_bp.R Normal file
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@ -0,0 +1,50 @@
#!/usr/bin/env Rscript
# load libraries
#########################################################
# TASK: function for basic barplot returning stability counts
#########################################################
# load libraries and functions
library(ggplot2)
theme_set(theme_grey())
#==========================================================
# my_stability_count(): basic barplots for stability counts
# input args
## df containing data to plot
## df column name containing stability outcome
## legend title
## ...opt args
#==========================================================
stability_count_bp <- function(plotdf
, df_colname
, leg_title
, axis_text_size = 25
, axis_label_size = 22
, leg_text_size = 20
, yaxis_title = "Number of nsSNPs"
, bp_plot_title = ""){
OutPlot_count = ggplot(plotdf, aes(x = eval(parse(text = df_colname)))) +
geom_bar(aes(fill = eval(parse(text = df_colname))), show.legend = TRUE) +
geom_label(stat = "count"
, aes(label = ..count..)
, color = "black"
, show.legend = FALSE
, size = 10) +
theme(axis.text.x = element_blank()
, axis.title.x = element_blank()
, axis.title.y = element_text(size = axis_label_size)
, axis.text.y = element_text(size = axis_text_size)
, 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)) +
labs(title = bp_plot_title
, y = yaxis_title) +
scale_fill_discrete(name = leg_title
, labels = c("Destabilising", "Stabilising"))
return(OutPlot_count)
}
#############################################################
# end of function
#############################################################

27
scripts/plotting/functions/test_functions.R Normal file
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@ -0,0 +1,27 @@
#=================
# Test function
#==================
#source("../plotting_data.R")
#infile = "/home/tanu/git/Data/streptomycin/output/gid_comb_stab_struc_params.csv"
#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]]
#------------------------------
# barplot for mscm stability
#------------------------------
#stability_count_bp(plotdf = my_df
# , df_colname = "duet_outcome"
# , leg_title = "DUET outcome")
#------------------------------
# barplot for ligand affinity
#------------------------------
#stability_count_bp(plotdf = my_df_u
# , df_colname = "ligand_outcome"
# , leg_title = "Ligand outcome"
# , bp_plot_title = "Sites < 10 Ang of ligand"
#)

4
scripts/plotting/myshiny/bp_app.R
View file

@ -17,7 +17,7 @@ library(dplyr)
# load functions
source("../plotting_globals.R")
source("../plotting_data.R")
source("my_stability_bp.R")
source("../functions/stability_count_bp.R")
###################################
# command line args :
@ -133,7 +133,7 @@ server <- function(input, output) {output$distPlot <- renderPlot({
p_title = "Sites < 10 Ang of ligand"}
# plot the basic barplots
my_stability_count(plotdf = data_plot
stability_count_bp(plotdf = data_plot
, df_colname = stability_colname,
, leg_title = leg_name
, bp_plot_title = p_title)