moved old logo plots scripts to redundant and updated running_plotting_scripts.txt to reflect these and how to run the single logo_plots.R to generate logo plots
This commit is contained in:
parent
f1a8fb583a
commit
639ccf1cd7
4 changed files with 34 additions and 42 deletions
257
scripts/plotting/redundant/logo_combined.R
Executable file
257
scripts/plotting/redundant/logo_combined.R
Executable file
|
|
@ -0,0 +1,257 @@
|
|||
#!/usr/bin/env Rscript
|
||||
#########################################################
|
||||
# TASK: producing logo-type plot showing
|
||||
# multiple muts per position coloured by aa property
|
||||
#########################################################
|
||||
#===========
|
||||
# output
|
||||
#===========
|
||||
|
||||
logo_combined_labelled = "logo_combined_labelled.svg"
|
||||
plot_logo_combined_labelled = paste0(plotdir,"/", logo_combined_labelled)
|
||||
|
||||
##########################################################################
|
||||
|
||||
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
# REASSIGNMENT
|
||||
my_df = merged_df3
|
||||
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
colnames(my_df)
|
||||
str(my_df)
|
||||
|
||||
#rownames(my_df) = my_df$mutation
|
||||
|
||||
c1 = unique(my_df$position)
|
||||
nrow(my_df)
|
||||
|
||||
# get freq count of positions so you can subset freq<1
|
||||
#require(data.table)
|
||||
setDT(my_df)[, mut_pos_occurrence := .N, by = .(position)] #189, 36
|
||||
|
||||
table(my_df$position)
|
||||
table(my_df$mut_pos_occurrence)
|
||||
|
||||
max_mut = max(table(my_df$position))
|
||||
|
||||
# extract freq_pos>1
|
||||
my_df_snp = my_df[my_df$mut_pos_occurrence!=1,]
|
||||
u = unique(my_df_snp$position)
|
||||
max_mult_mut = max(table(my_df_snp$position))
|
||||
|
||||
if (nrow(my_df_snp) == nrow(my_df) - table(my_df$mut_pos_occurrence)[[1]] ){
|
||||
|
||||
cat("PASS: positions with multiple muts extracted"
|
||||
, "\nNo. of mutations:", nrow(my_df_snp)
|
||||
, "\nNo. of positions:", length(u)
|
||||
, "\nMax no. of muts at any position", max_mult_mut)
|
||||
}else{
|
||||
cat("FAIL: positions with multiple muts could NOT be extracted"
|
||||
, "\nExpected:",nrow(my_df) - table(my_df$mut_pos_occurrence)[[1]]
|
||||
, "\nGot:", nrow(my_df_snp) )
|
||||
}
|
||||
|
||||
cat("\nNo. of sites with only 1 mutations:", table(my_df$mut_pos_occurrence)[[1]])
|
||||
|
||||
|
||||
########################################################################
|
||||
# end of data extraction and cleaning for_mychisq plots #
|
||||
########################################################################
|
||||
|
||||
#==============
|
||||
# matrix for_mychisq mutant type
|
||||
# frequency of mutant type by position
|
||||
#==============
|
||||
table(my_df_snp$mutant_type, my_df_snp$position)
|
||||
tab_mt = table(my_df_snp$mutant_type, my_df_snp$position)
|
||||
class(tab_mt)
|
||||
|
||||
# unclass to convert to matrix
|
||||
tab_mt = unclass(tab_mt)
|
||||
tab_mt = as.matrix(tab_mt, rownames = T)
|
||||
|
||||
#should be TRUE
|
||||
is.matrix(tab_mt)
|
||||
|
||||
rownames(tab_mt) #aa
|
||||
colnames(tab_mt) #pos
|
||||
|
||||
#**************
|
||||
# Plot 1: mutant logo
|
||||
#**************
|
||||
p0 = ggseqlogo(tab_mt
|
||||
, method = 'custom'
|
||||
, seq_type = 'aa') +
|
||||
#ylab('my custom height') +
|
||||
theme_logo()+
|
||||
scale_x_discrete(#breaks = 1:ncol(tab_mt)
|
||||
labels = as.numeric(colnames(tab_mt))
|
||||
, limits = factor(as.numeric(colnames(tab_mt))))+
|
||||
scale_y_continuous( breaks = 1:max_mult_mut
|
||||
, limits = c(0, max_mult_mut))
|
||||
|
||||
|
||||
#p0
|
||||
|
||||
# further customisation
|
||||
p1 = p0 + theme(axis.text.x = element_text(size = 16
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
, axis.text.y = element_blank()
|
||||
, legend.position = "none")
|
||||
#, axis.text.y = element_text(size = 20))
|
||||
#p1
|
||||
|
||||
#==============
|
||||
# matrix for wild type
|
||||
# frequency of wild type by position
|
||||
#==============
|
||||
tab_wt = table(my_df_snp$wild_type, my_df_snp$position); tab_wt
|
||||
tab_wt = unclass(tab_wt)
|
||||
|
||||
#remove wt duplicates
|
||||
wt = my_df_snp[, c("position", "wild_type")]
|
||||
wt = wt[!duplicated(wt),]
|
||||
|
||||
tab_wt = table(wt$wild_type, wt$position); tab_wt # should all be 1
|
||||
rownames(tab_wt)
|
||||
rownames(tab_wt)
|
||||
|
||||
#**************
|
||||
# Plot 2: wild_type logo
|
||||
#**************
|
||||
# sanity check: MUST BE TRUE
|
||||
|
||||
identical(colnames(tab_mt), colnames(tab_wt))
|
||||
identical(ncol(tab_mt), ncol(tab_wt))
|
||||
|
||||
p2 = ggseqlogo(tab_wt
|
||||
, method = 'custom'
|
||||
, seq_type = 'aa'
|
||||
#, col_scheme = "taylor"
|
||||
#, col_scheme = chemistry2
|
||||
) +
|
||||
#ylab('my custom height') +
|
||||
theme(axis.text.x = element_blank()
|
||||
, axis.text.y = element_blank()) +
|
||||
#theme_logo() +
|
||||
scale_x_discrete(breaks = 1:ncol(tab_wt)
|
||||
, labels = colnames(tab_wt))
|
||||
#p2
|
||||
|
||||
# further customise
|
||||
p3 = p2 +
|
||||
theme(legend.position = "bottom"
|
||||
#, legend.title = element_blank()
|
||||
, legend.title = element_text("Amino acid properties", size = 20)
|
||||
, legend.text = element_text(size = 20)
|
||||
, axis.text.x = element_text(size = 16, angle = 90)
|
||||
, axis.text.y = element_blank()
|
||||
, axis.title.y = element_blank()
|
||||
, axis.title.x = element_text(size = 22))+
|
||||
|
||||
labs(x= "Wild-type Position")
|
||||
|
||||
#p3
|
||||
#======================================================================
|
||||
# logo with OR
|
||||
#=======================================================================
|
||||
# quick checks
|
||||
colnames(my_df)
|
||||
str(my_df)
|
||||
|
||||
c1 = unique(my_df$position)
|
||||
nrow(my_df)
|
||||
cat("No. of rows in my_df:", nrow(my_df)
|
||||
, "\nDistinct positions corresponding to snps:", length(c1)
|
||||
, "\n===========================================================")
|
||||
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
# FIXME: Think and decide what you want to remove
|
||||
# mut_pos_occurence < 1 or sample_pos_occurrence <1
|
||||
|
||||
# get freq count of positions so you can subset freq<1
|
||||
require(data.table)
|
||||
#setDT(my_df)[, mut_pos_occurrence := .N, by = .(position)]
|
||||
|
||||
#extract freq_pos>1
|
||||
#my_df_snp = my_df[my_df$occurrence!=1,]
|
||||
|
||||
#u = unique(my_df_snp$position)
|
||||
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
||||
|
||||
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
# REASSIGNMENT to prevent changing code
|
||||
head(my_df_snp) #(positions with multiple snps) only
|
||||
length(unique(my_df_snp$position))
|
||||
|
||||
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
#=======================================================================
|
||||
#%% logo plots from dataframe
|
||||
|
||||
#############
|
||||
# PLOTS: ggseqlogo with custom height
|
||||
# https://omarwagih.github.io/ggseqlogo/
|
||||
#############
|
||||
foo = my_df_snp[, c("position", "mutant_type","duet_scaled", "or_mychisq"
|
||||
, "mut_prop_polarity", "mut_prop_water") ]
|
||||
|
||||
my_df_snp$log10or = log10(my_df_snp$or_mychisq)
|
||||
logo_data = my_df_snp[, c("position", "mutant_type", "or_mychisq", "log10or")]
|
||||
|
||||
logo_data_or = my_df_snp[, c("position", "mutant_type", "or_mychisq")]
|
||||
#wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
|
||||
wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = NA)
|
||||
|
||||
wide_df_or = as.matrix(wide_df_or)
|
||||
rownames(wide_df_or) = wide_df_or[,1]
|
||||
wide_df_or = wide_df_or[,-1]
|
||||
str(wide_df_or)
|
||||
|
||||
position_or = as.numeric(colnames(wide_df_or))
|
||||
|
||||
#===========================================
|
||||
#custom height (OR) logo plot: CORRECT x-axis labelling
|
||||
#============================================
|
||||
# custom height (OR) logo plot: yayy works
|
||||
logo_or = ggseqlogo(wide_df_or, method="custom", seq_type="aa") + ylab("my custom height") +
|
||||
theme(axis.text.x = element_text(size = 15
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
, axis.text.y = element_text(size = 18
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.y = element_text(size = 18)
|
||||
, axis.title.x = element_blank()
|
||||
, legend.position = "none")+
|
||||
scale_x_discrete( labels = position_or
|
||||
, limits = factor(1:length(position_or))) +
|
||||
scale_y_discrete(breaks = c(50, 150, 250, 350)
|
||||
, labels = c(50, 150, 250, 350)
|
||||
, limits = c(50, 150, 250, 350)
|
||||
) +
|
||||
xlab("Position") +
|
||||
ylab("Odds Ratio")
|
||||
|
||||
#logo_or
|
||||
########################################################################
|
||||
|
||||
#=============================
|
||||
# combine plots for output
|
||||
#=============================
|
||||
cat("Output plot:", plot_logo_combined_labelled)
|
||||
svg(plot_logo_combined_labelled, width = 25, height = 10)
|
||||
|
||||
OutPlot2 = cowplot::plot_grid(logo_or, p1, p3
|
||||
, nrow = 3
|
||||
, align = "hv"
|
||||
#, labels = c("(a)","(b)", "(c)")
|
||||
, labels = "AUTO"
|
||||
, rel_heights = c(3/8, 3/8, 1.5/8)
|
||||
, rel_widths = c(0.85, 1, 1)
|
||||
, label_size = 25)
|
||||
|
||||
print(OutPlot2)
|
||||
#dev.off()
|
||||
118
scripts/plotting/redundant/logo_multiple_muts.R
Executable file
118
scripts/plotting/redundant/logo_multiple_muts.R
Executable file
|
|
@ -0,0 +1,118 @@
|
|||
#!/usr/bin/env Rscript
|
||||
getwd()
|
||||
setwd("~/git/LSHTM_analysis/scripts/plotting")
|
||||
getwd()
|
||||
source("Header_TT.R")
|
||||
|
||||
spec = matrix(c(
|
||||
"drug" , "d", 1, "character",
|
||||
"gene" , "g", 1, "character",
|
||||
"data_file1" , "fa", 2, "character",
|
||||
"data_file2" , "fb", 2, "character"
|
||||
), byrow = TRUE, ncol = 4)
|
||||
|
||||
opt = getopt(spec)
|
||||
|
||||
drug = opt$drug
|
||||
gene = opt$gene
|
||||
infile_params = opt$data_file1
|
||||
infile_metadata = opt$data_file2
|
||||
|
||||
if(is.null(drug)|is.null(gene)) {
|
||||
stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
|
||||
}
|
||||
|
||||
#===========
|
||||
# Input
|
||||
#===========
|
||||
|
||||
source("get_plotting_dfs.R")
|
||||
|
||||
#===========
|
||||
# output
|
||||
#===========
|
||||
logo_multiple_muts = "logo_multiple_muts.svg"
|
||||
plot_logo_multiple_muts = paste0(plotdir,"/", logo_multiple_muts)
|
||||
|
||||
#*********************
|
||||
# Plot 1: mutant logo
|
||||
#*********************
|
||||
p0 = ggseqlogo(tab_mt
|
||||
, method = 'custom'
|
||||
, seq_type = 'aa') +
|
||||
#ylab('my custom height') +
|
||||
theme(axis.text.x = element_blank()) +
|
||||
theme(text=element_text(family="FreeSans"))+
|
||||
theme_logo()+
|
||||
scale_x_continuous(breaks = 1:ncol(tab_mt)
|
||||
, labels = colnames(tab_mt))+
|
||||
scale_y_continuous( breaks = 1:max_mult_mut
|
||||
, limits = c(0, max_mult_mut))
|
||||
|
||||
p0
|
||||
cat('\nDone: p0')
|
||||
|
||||
# further customisation
|
||||
mut_logo_p = p0 + theme(legend.position = "none"
|
||||
, legend.title = element_blank()
|
||||
, legend.text = element_text(size = 20)
|
||||
, axis.text.x = element_text(size = 17, angle = 90)
|
||||
, axis.text.y = element_blank())
|
||||
#mut_logo_p
|
||||
cat('\nDone: p0+mut_logo_p')
|
||||
|
||||
#***********************
|
||||
# Plot 2: wild_type logo
|
||||
#***********************
|
||||
p2 = ggseqlogo(tab_wt
|
||||
, method = 'custom'
|
||||
, seq_type = 'aa'
|
||||
#, col_scheme = "taylor"
|
||||
#, col_scheme = chemistry2
|
||||
) +
|
||||
#ylab('my custom height') +
|
||||
theme(text=element_text(family="FreeSans"))+
|
||||
theme(axis.text.x = element_blank()
|
||||
, axis.text.y = element_blank()) +
|
||||
theme_logo() +
|
||||
scale_x_continuous(breaks = 1:ncol(tab_wt)
|
||||
, labels = colnames(tab_wt))
|
||||
#p2
|
||||
cat('\nDone: p2 done')
|
||||
|
||||
# further customise
|
||||
wt_logo_p = p2 +
|
||||
theme(legend.position = "bottom"
|
||||
#, legend.title = element_blank()
|
||||
, legend.title = element_text("Amino acid properties", size = 20)
|
||||
, legend.text = element_text(size = 20)
|
||||
, axis.text.x = element_text(size = 17, angle = 90)
|
||||
, axis.text.y = element_blank()
|
||||
, axis.title.x = element_text(size = 22))+
|
||||
|
||||
labs(x= "Position")
|
||||
|
||||
#wt_logo_p
|
||||
cat('\nDone: wt_logo_p')
|
||||
|
||||
#------------------------------------
|
||||
# Now combine using cowplot
|
||||
# which ensures the plots are aligned
|
||||
#------------------------------------
|
||||
#suppressMessages( require(cowplot) )
|
||||
cat('\nDone: wt_logo_p')
|
||||
|
||||
#plot_grid(p1, p3, ncol = 1, align = 'v')
|
||||
cat('\nDone: mut_logo_p + wt_logo_p')
|
||||
|
||||
# colour scheme: https://rdrr.io/cran/ggseqlogo/src/R/col_schemes.r
|
||||
cat("\nOutput plot:", plot_logo_multiple_muts, "\n")
|
||||
svg(plot_logo_multiple_muts, width = 32, height = 10)
|
||||
|
||||
mult_muts_combined = cowplot::plot_grid(mut_logo_p, wt_logo_p
|
||||
, nrow = 2
|
||||
, align = "v"
|
||||
, rel_heights = c(3/4, 1/4))
|
||||
|
||||
print(mult_muts_combined)
|
||||
#dev.off()
|
||||
106
scripts/plotting/redundant/logo_plot.R
Executable file
106
scripts/plotting/redundant/logo_plot.R
Executable file
|
|
@ -0,0 +1,106 @@
|
|||
#!/usr/bin/env Rscript
|
||||
getwd()
|
||||
setwd("~/git/LSHTM_analysis/scripts/plotting")
|
||||
getwd()
|
||||
source("Header_TT.R")
|
||||
|
||||
spec = matrix(c(
|
||||
"drug" , "d", 1, "character",
|
||||
"gene" , "g", 1, "character",
|
||||
"data_file1" , "fa", 2, "character",
|
||||
"data_file2" , "fb", 2, "character"
|
||||
), byrow = TRUE, ncol = 4)
|
||||
|
||||
opt = getopt(spec)
|
||||
|
||||
drug = opt$drug
|
||||
gene = opt$gene
|
||||
infile_params = opt$data_file1
|
||||
infile_metadata = opt$data_file2
|
||||
|
||||
if(is.null(drug)|is.null(gene)) {
|
||||
stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
|
||||
}
|
||||
|
||||
#===========
|
||||
# Input
|
||||
#===========
|
||||
|
||||
source("get_plotting_dfs.R")
|
||||
|
||||
#===========
|
||||
# output
|
||||
#===========
|
||||
logo_or_plotname = "logo_or_plot.svg"
|
||||
plot_logo_or = paste0(plotdir,"/", logo_or_plotname)
|
||||
|
||||
logo_logOR_plotname = "logo_logOR_plot.svg"
|
||||
plot_logo_logOR = paste0(plotdir,"/", logo_logOR_plotname)
|
||||
|
||||
##############################################################################
|
||||
|
||||
#================================
|
||||
# Logo plot: custom height (OR)
|
||||
#================================
|
||||
cat("Logo plot with OR as y axis:", plot_logo_or)
|
||||
svg(plot_logo_or, width = 30 , height = 6)
|
||||
|
||||
logo_or = ggseqlogo(wide_df_or
|
||||
, method = "custom"
|
||||
, seq_type = "aa") + ylab("my custom height") +
|
||||
theme( axis.text.x = element_text(size = 12
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
, axis.text.y = element_text(size = 22
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.y = element_text(size = 25)
|
||||
, axis.title.x = element_text(size = 20)
|
||||
#, legend.position = "bottom") +
|
||||
, legend.position = "none")+
|
||||
#, legend.text = element_text(size = 15)
|
||||
#, legend.title = element_text(size = 15))+
|
||||
scale_x_discrete("Position"
|
||||
#, breaks
|
||||
, labels = position_or
|
||||
, limits = factor(1:length(position_or))) +
|
||||
ylab("Odds Ratio")
|
||||
|
||||
print(logo_or)
|
||||
dev.off()
|
||||
|
||||
#=======================================
|
||||
# Logo plot: custom height (Log10 OR)
|
||||
#=======================================
|
||||
cat("Logo plot with log10 OR as y axis:", plot_logo_logOR)
|
||||
svg(plot_logo_logOR, width = 30 , height = 6)
|
||||
|
||||
logo_logOR = ggseqlogo(wide_df_logor_m
|
||||
, method = "custom"
|
||||
, seq_type="aa") + ylab("my custom height") +
|
||||
theme(legend.position = "bottom"
|
||||
, axis.text.x = element_text(size = 13
|
||||
, angle = 90
|
||||
, hjust = 1
|
||||
, vjust = 0.4)
|
||||
, axis.text.y = element_text(size = 20
|
||||
, angle = 0
|
||||
, hjust = 1
|
||||
, vjust = 0)
|
||||
, axis.title.y = element_text(size = 25)
|
||||
, axis.title.x = element_text(size = 20))+
|
||||
scale_x_discrete("Position"
|
||||
#, breaks
|
||||
, labels = position_logor
|
||||
, limits = factor(1:length(position_logor)))+
|
||||
ylab("Log (Odds Ratio)") +
|
||||
scale_y_continuous(limits = c(0, 9))
|
||||
|
||||
print(logo_logOR)
|
||||
dev.off()
|
||||
|
||||
######################################################################=
|
||||
# End of script
|
||||
######################################################################=
|
||||
Loading…
Add table
Add a link
Reference in a new issue