142 lines
4.4 KiB
R
142 lines
4.4 KiB
R
#!/usr/bin/env Rscript
|
|
#########################################################
|
|
# TASK: Script to format data for Logo_plots
|
|
#########################################################
|
|
#-------------------------
|
|
# choose df for logoplot
|
|
#-------------------------
|
|
logo_data = merged_df3
|
|
#logo_data = merged_df3_comp
|
|
|
|
# quick checks
|
|
colnames(logo_data)
|
|
str(logo_data)
|
|
|
|
c1 = unique(logo_data$position)
|
|
nrow(logo_data)
|
|
cat("No. of rows in my_data:", nrow(logo_data)
|
|
, "\nDistinct positions corresponding to snps:", length(c1)
|
|
, "\n===========================================================")
|
|
#=======================================================================
|
|
#==================
|
|
# logo data: OR
|
|
#==================
|
|
foo = logo_data[, c("position"
|
|
, "mutant_type","duet_scaled", "or_mychisq"
|
|
, "mut_prop_polarity", "mut_prop_water")]
|
|
|
|
logo_data$log10or = log10(logo_data$or_mychisq)
|
|
logo_data_plot = logo_data[, c("position"
|
|
, "mutant_type", "or_mychisq", "log10or")]
|
|
|
|
logo_data_plot_or = logo_data[, c("position", "mutant_type", "or_mychisq")]
|
|
wide_df_or = logo_data_plot_or %>% spread(position, or_mychisq, fill = 0.0)
|
|
|
|
wide_df_or = as.matrix(wide_df_or)
|
|
rownames(wide_df_or) = wide_df_or[,1]
|
|
dim(wide_df_or)
|
|
wide_df_or = wide_df_or[,-1]
|
|
str(wide_df_or)
|
|
|
|
position_or = as.numeric(colnames(wide_df_or))
|
|
|
|
#==================
|
|
# logo data: logOR
|
|
#==================
|
|
logo_data_plot_logor = logo_data[, c("position", "mutant_type", "log10or")]
|
|
wide_df_logor <- logo_data_plot_logor %>% spread(position, log10or, fill = 0.0)
|
|
|
|
wide_df_logor = as.matrix(wide_df_logor)
|
|
|
|
rownames(wide_df_logor) = wide_df_logor[,1]
|
|
wide_df_logor = subset(wide_df_logor, select = -c(1) )
|
|
colnames(wide_df_logor)
|
|
wide_df_logor_m = data.matrix(wide_df_logor)
|
|
|
|
rownames(wide_df_logor_m)
|
|
colnames(wide_df_logor_m)
|
|
|
|
position_logor = as.numeric(colnames(wide_df_logor_m))
|
|
|
|
#===============================
|
|
# logo data: multiple nsSNPs (>1)
|
|
#=================================
|
|
#require(data.table)
|
|
|
|
# get freq count of positions so you can subset freq<1
|
|
setDT(logo_data)[, mut_pos_occurrence := .N, by = .(position)]
|
|
|
|
table(logo_data$position)
|
|
table(logo_data$mut_pos_occurrence)
|
|
|
|
max_mut = max(table(logo_data$position))
|
|
|
|
# extract freq_pos > 1
|
|
my_data_snp = logo_data[logo_data$mut_pos_occurrence!=1,]
|
|
u = unique(my_data_snp$position)
|
|
max_mult_mut = max(table(my_data_snp$position))
|
|
|
|
if (nrow(my_data_snp) == nrow(logo_data) - table(logo_data$mut_pos_occurrence)[[1]] ){
|
|
|
|
cat("PASS: positions with multiple muts extracted"
|
|
, "\nNo. of mutations:", nrow(my_data_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(logo_data) - table(logo_data$mut_pos_occurrence)[[1]]
|
|
, "\nGot:", nrow(my_data_snp) )
|
|
}
|
|
|
|
cat("\nNo. of sites with only 1 mutations:", table(logo_data$mut_pos_occurrence)[[1]])
|
|
|
|
#--------------------------------------
|
|
# matrix for_mychisq mutant type
|
|
# frequency of mutant type by position
|
|
#---------------------------------------
|
|
table(my_data_snp$mutant_type, my_data_snp$position)
|
|
tab_mt = table(my_data_snp$mutant_type, my_data_snp$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
|
|
|
|
#-------------------------------------
|
|
# matrix for wild type
|
|
# frequency of wild type by position
|
|
#-------------------------------------
|
|
tab_wt = table(my_data_snp$wild_type, my_data_snp$position); tab_wt
|
|
tab_wt = unclass(tab_wt)
|
|
|
|
# remove wt duplicates
|
|
wt = my_data_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)
|
|
|
|
identical(colnames(tab_mt), colnames(tab_wt))
|
|
identical(ncol(tab_mt), ncol(tab_wt))
|
|
|
|
#----------------------------------
|
|
# logo data OR: multiple nsSNPs (>1)
|
|
#----------------------------------
|
|
logo_data_or_mult = my_data_snp[, c("position", "mutant_type", "or_mychisq")]
|
|
#wide_df_or = logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
|
|
wide_df_or_mult = logo_data_or_mult %>% spread(position, or_mychisq, fill = NA)
|
|
|
|
wide_df_or_mult = as.matrix(wide_df_or_mult)
|
|
rownames(wide_df_or_mult) = wide_df_or_mult[,1]
|
|
wide_df_or_mult = wide_df_or_mult[,-1]
|
|
str(wide_df_or_mult)
|
|
|
|
position_or_mult = as.numeric(colnames(wide_df_or_mult))
|