405 lines
14 KiB
R
405 lines
14 KiB
R
library(Logolas)
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library(ggseqlogo)
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source("~/git/LSHTM_analysis/scripts/functions/my_logolas.R")
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# data msa: mut
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my_data = read.csv("/home/tanu/git/Misc/practice_plots/pnca_msa_eg2.csv", header = F) #15 cols only
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msaSeq_mut = my_data$V1
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# data msa: wt
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gene = "pncA"
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drug = "pyrazinamide"
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indir = paste0("~/git/Data/", drug , "/input/")
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in_filename_fasta = paste0(tolower(gene), "2_f2.fasta")
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infile_fasta = paste0(indir, in_filename_fasta)
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cat("\nInput fasta file for WT: ", infile_fasta, "\n")
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msa2 = read.csv(infile_fasta, header = F)
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head(msa2)
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cat("\nLength of WT fasta:", nrow(msa2))
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#wt_seq = msa2$V1
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#head(wt_seq)
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msaSeq_wt = msa2$V1
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###########################################
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PlotLogolasMSA <- function(msaSeq_mut # chr vector
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, msaSeq_wt # chr vector
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, msa_method = c("custom") # will be c("EDLogo", "Logo)#
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, EDLogo_score = c("log")# can be: "log-odds", "diff", "probKL", "ratio", "unscaled_log", "wKL"
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, bg_prob = NULL
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, my_logo_col = "chemistry"
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, plot_positions = c(1, 10, 14, 8)
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, y_breaks
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, x_lab = "Wild-type position"
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, y_lab = ""
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, x_ats = 13 # text size
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, x_tangle = 90 # text angle
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, x_axis_offset = 0.05 # dist b/w y-axis and plot start
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, x_axis_offset_filtered = 0.2
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, y_axis_offset = 0.05
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, y_ats = 13
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, y_tangle = 0
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, x_tts = 13 # title size
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, y_tts = 13
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, leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
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, leg_dir = "horizontal" #can be vertical or horizontal
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, leg_ts = 16 # leg text size
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, leg_tts = 16 # leg title size
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)
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{
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dash_control = list()
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dash_control_default <- list(concentration = NULL, mode = NULL,
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optmethod = "mixEM", sample_weights = NULL, verbose = FALSE,
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bf = TRUE, pi_init = NULL, squarem_control = list(),
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dash_control = list(), reportcov = FALSE)
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dash_control <- modifyList(dash_control_default, dash_control)
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############################################
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# Data processing for logo plot for nsSNPS
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###########################################
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cat("\nLength of MSA", length(msaSeq_mut)
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, "\nlength of WT seq:", length(msaSeq_wt))
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cat("\n======================="
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, "\nPlotting entire MSA"
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, "\n========================")
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#--------------------------
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# Getting PFM: mutant MSA
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#--------------------------
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pfm_mut <- Biostrings::consensusMatrix(msaSeq_mut)
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colnames(pfm_mut) <- 1:dim(pfm_mut)[2]
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pfm_mut_scaled <- do.call(dash, append(list(comp_data = pfm_mut),
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dash_control))$posmean
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logo_mut_h = get_logo_heights(pfm_mut_scaled
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, bg = bg_prob
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, score = EDLogo_score)
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logo_mut_h$pos_ic
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logo_mut_h$neg_ic
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# TODO: Add sanity check!
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#<...
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#...>
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pos_mutM = logo_mut_h[['table_mat_pos_norm']]; pos_mutM
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pos_mutS = logo_mut_h$pos_ic; pos_mutS
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pos_mutED = t(pos_mutS*t(pos_mutM)); pos_mutED
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neg_mutM = logo_mut_h[['table_mat_neg_norm']]*(-1)
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neg_mutS = logo_mut_h$neg_ic; neg_mutS
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neg_mutED = t(neg_mutS*t(neg_mutM)); neg_mutED
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combED_mutM = pos_mutED + neg_mutED
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# Construct the x-axis: mutant MSA
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msa_all_pos = as.numeric(colnames(combED_mutM))
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#---------------------
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# Getting PFM: WT
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#---------------------
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pfm_wt <- Biostrings::consensusMatrix(msaSeq_wt)
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colnames(pfm_wt) <- 1:dim(pfm_wt)[2]
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pfm_wt_scaled <- do.call(dash, append(list(comp_data = pfm_wt),
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dash_control))$posmean
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logo_wt_h = get_logo_heights(pfm_wt_scaled
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, bg = bg_prob
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, score = EDLogo_score)
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logo_wt_h$pos_ic
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logo_wt_h$neg_ic
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pos_wtM = logo_wt_h[['table_mat_pos_norm']]; pos_wtM
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pos_wtS = logo_wt_h$pos_ic; pos_wtS
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pos_wtED = t(pos_wtS*t(pos_wtM)); pos_wtED
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neg_wtM = logo_wt_h[['table_mat_neg_norm']]*(-1)
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neg_wtS = logo_wt_h$neg_ic; neg_wtS
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neg_wtED = t(neg_wtS*t(neg_wtM)); neg_wtED
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combED_wtM = pos_wtED + neg_wtED
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# Construct the x-axis: mutant MSA
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wt_all_pos = as.numeric(colnames(combED_wtM))
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if(missing(plot_positions)){
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#------------------------------
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# MSA mut: All, no filtering
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#-------------------------------
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cat("\n==========================================="
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, "\nGenerated PFM mut: No filtering"
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, "\n===========================================")
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plot_mut_edM = combED_mutM
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#------------------------------
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# MSA WT: All, no filtering
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#-------------------------------
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cat("\n==========================================="
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, "\nGenerated PFM WT: No filtering"
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, "\n===========================================")
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plot_wt_edM = combED_wtM
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}else{
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#------------------------------
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# PFM mut: Filtered positions
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#-------------------------------
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cat("\n==========================================="
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, "\nGenerating PFM MSA: filtered positions"
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, "\n==========================================="
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, "\nUser specified plotting positions for MSA:"
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, "\nThese are:\n", plot_positions
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, "\nSorting plot positions...")
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plot_positions = sort(plot_positions)
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cat("\nPlotting positions sorted:\n"
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, plot_positions)
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if ( all(plot_positions%in%msa_all_pos) && all(plot_positions%in%wt_all_pos) ){
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cat("\nAll positions within range"
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, "\nFiltering positions as specified..."
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, "\nNo. of positions in plot:", length(plot_positions))
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i_extract = plot_positions
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plot_mut_edM = combED_mutM[, i_extract]
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plot_wt_edM = combED_wtM[, i_extract]
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}else{
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cat("\nNo. of positions selected:", length(plot_positions))
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i_ofr = plot_positions[!plot_positions%in%msa_all_pos]
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cat("\n1 or more plot_positions out of range..."
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, "\nThese are:\n", i_ofr
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, "\nQuitting! Resubmit with correct plot_positions")
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quit()
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}
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}
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# Construct the y-axis: Calculating
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cat("\n-------------------------"
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, "\nConstructing y-axis:"
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, "\nUser did not provide"
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,"\n--------------------------")
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if (missing(y_breaks)){
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ylim_low <- floor(min(combED_mutM)); ylim_low
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if( ylim_low == 0){
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ylim_low = ylim_low
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cat("\nY-axis lower limit:", ylim_low)
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y_rlow = seq(0, ylim_low, length.out = 3); y_rlow
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ylim_up <- ceiling(max(combED_mutM)) + 4; ylim_up
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cat("\nY-axis upper limit:", ylim_up)
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y_rup = seq(0, ylim_up, by = 2); y_rup
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}else{
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ylim_low = ylim_low + (-0.5)
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cat("\nY-axis lower limit is <0:", ylim_low)
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y_rlow = seq(0, ylim_low, length.out = 3); y_rlow
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ylim_up <- ceiling(max(combED_mutM)) + 3; ylim_up
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cat("\nY-axis upper limit:", ylim_up)
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y_rup = seq(0, ylim_up, by = 3); y_rup
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}
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#ylim_scale <- unique(sort(c(y_rlow, y_rup, ylim_up))); ylim_scale
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ylim_scale <- unique(sort(c(y_rlow, y_rup))); ylim_scale
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cat("\nY-axis generated: see below"
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, "\n"
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, ylim_scale)
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}else{
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# Construct the y-axis: User provided
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cat("\n-------------------------"
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, "\nConstructing y-axis:"
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, "\nUser provided"
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,"\n--------------------------")
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ylim_scale = sort(y_breaks)
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ylim_low = min(ylim_scale); ylim_low
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ylim_up = max(ylim_scale); ylim_up
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}
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else {
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}
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######################################
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# Generating plots for muts and wt
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#####################################
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if (my_logo_col %in% c('clustalx','taylor')) {
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cat("\nSelected colour scheme:", my_logo_col
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, "\nUsing black theme\n")
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theme_bgc = "black"
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xfont_bgc = "white"
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yfont_bgc = "white"
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xtt_col = "white"
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ytt_col = "white"
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}
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if (my_logo_col %in% c('chemistry', 'hydrophobicity')) {
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cat("\nstart of MSA"
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, '\nSelected colour scheme:', my_logo_col
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, "\nUsing grey theme")
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theme_bgc = "grey"
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xfont_bgc = "black"
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yfont_bgc = "black"
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xtt_col = "black"
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ytt_col = "black"
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}
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#####################################
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# Generating logo plots for nsSNPs
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#####################################
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PlotlogolasL <- list()
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#-------------------
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# Mutant logo plot
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#-------------------
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p0 = ggseqlogo(plot_mut_edM
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#, facet = "grid"
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, method = msa_method
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, col_scheme = my_logo_col
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, seq_type = 'auto') +
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theme(legend.position = leg_pos
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, legend.direction = leg_dir
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#, legend.title = element_blank()
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, legend.title = element_text(size = leg_tts
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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, axis.text.x = element_text(size = x_ats
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, angle = x_tangle
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, hjust = 1
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, vjust = 0.4
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, colour = xfont_bgc)
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#, axis.text.y = element_blank()
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, axis.text.y = element_text(size = y_ats
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, angle = y_tangle
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, hjust = 1
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, vjust = -1.0
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, colour = yfont_bgc)
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, axis.title.x = element_text(size = x_tts
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, colour = xtt_col)
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, plot.background = element_rect(fill = theme_bgc))+
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xlab(x_lab)
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if (missing(plot_positions)){
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ed_mut_logo_P = p0 +
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scale_x_discrete(breaks = msa_all_pos
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, expand = c(x_axis_offset,0)
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, labels = msa_all_pos
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, limits = factor(msa_all_pos))+
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scale_y_continuous(limits = c(ylim_low, ylim_up)
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, breaks = ylim_scale
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, expand = c(0,y_axis_offset)) +
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geom_hline(yintercept = 0
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, linetype = "solid"
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, color = "grey"
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, size = 1)
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}else{
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ed_mut_logo_P = p0 +
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#scale_y_continuous(expand = c(0,0.09)) +
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scale_y_continuous(limits = c(ylim_low, ylim_up)
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, breaks = ylim_scale
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, expand = c(0,y_axis_offset))+
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scale_x_discrete(breaks = i_extract
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, expand = c(x_axis_offset_filtered,0)
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, labels = i_extract
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, limits = factor(i_extract)) +
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geom_hline(yintercept = 0
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, linetype = "solid"
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, color = "grey"
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, size = 1)
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}
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cat('\nDone: MSA plot for mutations')
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#return(msa_mut_logoP)
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PlotlogolasL[['ed_mut_logoP']] <- ed_mut_logo_P
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#---------------------------------
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# Wild-type MSA: gene_fasta file
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#---------------------------------
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p1 = ggseqlogo(plot_wt_edM
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#, facet = "grid"
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, method = msa_method
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, col_scheme = my_logo_col
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, seq_type = 'aa') +
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theme(legend.position = "none"
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, legend.direction = leg_dir
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#, legend.title = element_blank()
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, legend.title = element_text(size = leg_tts
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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, axis.text.x = element_text(size = x_ats
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, angle = x_tangle
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, hjust = 1
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, vjust = 0.4
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, colour = xfont_bgc)
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, axis.text.y = element_blank()
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, axis.title.x = element_text(size = x_tts
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, colour = xtt_col)
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, plot.background = element_rect(fill = theme_bgc)) +
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ylab("") + xlab("Wild-type position")
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if (missing(plot_positions)){
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ed_wt_logo_P = p1 +
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scale_x_discrete(breaks = wt_all_pos
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, expand = c(x_axis_offset,0)
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, labels = wt_all_pos
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, limits = factor(wt_all_pos))
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}else{
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ed_wt_logo_P = p1 +
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scale_y_continuous(expand = c(0,0.09)) +
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scale_x_discrete(breaks = i_extract
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, expand = c(x_axis_offset_filtered, 0)
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, labels = i_extract
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, limits = factor(i_extract))
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}
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cat('\nDone: MSA plot for WT')
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#return(msa_wt_logoP)
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PlotlogolasL[['ed_wt_logoP']] <- ed_wt_logo_P
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#=========================================
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# Output
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# Combined plot: logo ED plot
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# customised for ggseqlogo
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#=========================================
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cat('\nDone: ed_mut_logoP + ed_wt_logoP')
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# colour scheme: https://rdrr.io/cran/ggseqlogo/src/R/col_schemes.r
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#cat("\nOutput plot:", LogoSNPs_comb, "\n")
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#svg(LogoSNPs_combined, width = 32, height = 10)
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LogoED_comb = cowplot::plot_grid(PlotlogolasL[['ed_mut_logoP']]
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, PlotlogolasL[['ed_wt_logoP']]
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, nrow = 2
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, align = "v"
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, rel_heights = c(3/4, 1/4))
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return(LogoED_comb)
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}
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