added my_logolas.R
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febb8f0f7f
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5 changed files with 1423 additions and 93 deletions
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@ -27,6 +27,7 @@ LogoPlotMSA <- function(msaSeq_mut
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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 = 0.07 # dist b/w y-axis and plot start
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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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@ -47,42 +48,66 @@ LogoPlotMSA <- function(msaSeq_mut
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if(missing(plot_positions)){
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#if(is.null(plot_positions)){
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cat("\nPlotting entire MSA")
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cat("\n======================="
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, "\nPlotting entire MSA"
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, "\n========================")
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msa_seq_plot = msaSeq_mut
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msa_all_interim = sapply(msa_seq_plot, function(x) unlist(strsplit(x,"")))
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msa_all_interimDF = data.frame(msa_all_interim)
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msa_all_pos = as.numeric(rownames(msa_all_interimDF))
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wt_seq_plot = msaSeq_wt
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wt_all_interim = sapply(wt_seq_plot, function(x) unlist(strsplit(x,"")))
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wt_all_interimDF = data.frame(wt_all_interim)
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wt_all_pos = as.numeric(rownames(wt_all_interimDF))
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} else {
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cat("\nUser specified plotting positions for MSA:"
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, "These are:", plot_positions)
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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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#-----------
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# MSA: mut
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#-----------
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cat("\nGenerating MSA: filtered positions")
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msa_interim = sapply(msaSeq_mut, function(x) unlist(strsplit(x,"")))
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cat("\n==========================================="
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, "\nGenerating MSA: filtered positions"
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, "\n===========================================")
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if (any(is.na(msa_interim[plot_positions]))){
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cat("Plot_positions selected:", length(plot_positions))
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i_ofr = plot_positions[is.na(msa_interim[plot_positions])]
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cat("\nIndex out of range: 1 or more"
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, "\nThese are:", i_ofr
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, "\nOmitting these and proceeding...")
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i_extract = na.omit(msa_interim[plot_positions])
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cat("\nFinal positions being plottted:", length(i_extract)
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, "\nNo. of positions dropped from request:", length(i_ofr))
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}else{
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msa_interim = sapply(msaSeq_mut, function(x) unlist(strsplit(x,"")))
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msa_interimDF = data.frame(msa_interim)
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msa_pos = as.numeric(rownames(msa_interimDF))
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if (all(plot_positions%in%msa_pos)){
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cat("\nAll positions within range"
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, "\nProceeing with generating requested position MSA seqs...")
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, "\nProceeding with generating requested position MSA seqs..."
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, "\nNo. of positions in plot:", length(plot_positions))
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i_extract = plot_positions
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dfP1 = msa_interimDF[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_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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#i_extract = plot_positions[plot_positions%in%msa_pos]
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#cat("\nFinal no. of positions being plottted:", length(i_extract)
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# , "\nNo. of positions dropped from request:", length(i_ofr))
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quit()
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}
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matP1 = msa_interim[i_extract, 1:ncol(msa_interim)]
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dfP1 = data.frame(t(matP1))
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#matP1 = msa_interim[i_extract, 1:ncol(msa_interim)]
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#dfP1 = msa_interimDF[i_extract,]
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dfP1 = data.frame(t(dfP1))
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names(dfP1) = i_extract
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cols_to_paste = names(dfP1)
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dfP1['chosen_seq'] = apply( dfP1[ , cols_to_paste]
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dfP1['chosen_seq'] = apply(dfP1[ , cols_to_paste]
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, 1
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, paste, sep = ''
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, collapse = "")
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@ -92,44 +117,46 @@ LogoPlotMSA <- function(msaSeq_mut
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#-----------
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# WT: fasta
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#-----------
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cat("\nGenerating WT fasta: filtered positions")
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cat("\n========================================="
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, "\nGenerating WT fasta: filtered positions"
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,"\n===========================================")
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wt_interim = sapply(msaSeq_wt, function(x) unlist(strsplit(x,"")))
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if (any(is.na(wt_interim[plot_positions]))){
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cat("Plot_positions selected:", length(plot_positions))
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i2_ofr = plot_positions[is.na(wt_interim[plot_positions])]
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cat("\nIndex out of range: 1 or more"
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, "\nThese are:", i2_ofr
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, "\nOmitting these and proceeding...")
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i2_extract = na.omit(wt_interim[plot_positions])
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cat("\nFinal positions being plottted:", length(i2_extract)
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, "\nNo. of positions dropped from request:", length(i2_ofr))
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}else{
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wt_interimDF = data.frame(wt_interim)
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wt_pos = as.numeric(rownames(wt_interimDF))
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if (all(plot_positions%in%wt_pos)){
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cat("\nAll positions within range"
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, "\nProceeing with generating requested position MSA seqs...")
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, "\nProceeding with generating requested position MSA seqs..."
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, "\nplot positions:", length(plot_positions))
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i2_extract = plot_positions
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}else{
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cat("\nNo. of positions selected:", length(plot_positions))
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i2_ofr = plot_positions[!plot_positions%in%wt_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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#i2_extract = plot_positions[plot_positions%in%wt_pos]
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#cat("\nFinal no. of positions being plottted:", length(i2_extract)
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# , "\nNo. of positions dropped from request:", length(i2_ofr))
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quit()
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}
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matP2 = wt_interim[i_extract, 1:ncol(wt_interim)]
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dfP2 = data.frame(t(matP2))
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#matP1 = msa_interim[i_extract, 1:ncol(msa_interim)]
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dfP2 = wt_interimDF[i2_extract,]
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dfP2 = data.frame(t(dfP2))
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names(dfP2) = i2_extract
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cols_to_paste_P2 = names(dfP2)
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dfP2['chosen_seq'] = apply( dfP2[ , cols_to_paste_P2]
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cols_to_paste2 = names(dfP2)
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dfP2['chosen_seq'] = apply( dfP2[ , cols_to_paste2]
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, 1
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, paste, sep = ''
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, collapse = "")
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wt_seq_plot = dfP2$chosen_seq
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}
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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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######################################
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# Generating plots for muts and wt
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#####################################
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LogoPlotMSAL <- list()
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if (my_logo_col %in% c('clustalx','taylor')) {
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@ -144,8 +171,9 @@ LogoPlotMSA <- function(msaSeq_mut
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}
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if (my_logo_col %in% c('chemistry', 'hydrophobicity')) {
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cat('\nSelected colour scheme:', my_logo_col
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, "\nUsing grey theme")
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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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@ -192,18 +220,22 @@ LogoPlotMSA <- function(msaSeq_mut
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xlab(x_lab)
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if (missing(plot_positions)){
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msa_mut_logo_P = p0
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msa_mut_logo_P = p0 +
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scale_x_discrete(breaks = msa_all_pos
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, expand = c(0.02,0)
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, labels = msa_all_pos
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, limits = factor(msa_all_pos))
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}else{
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msa_mut_logo_P = p0 +
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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(0.09,0)
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, expand = c(x_axis_offset,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_mut_logo_P')
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cat('\nDone: MSA plot for mutations')
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#return(msa_mut_logoP)
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LogoPlotMSAL[['msa_mut_logoP']] <- msa_mut_logo_P
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@ -237,20 +269,24 @@ LogoPlotMSA <- function(msaSeq_mut
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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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msa_wt_logo_P = p1
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msa_wt_logo_P = p1 +
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scale_x_discrete(breaks = wt_all_pos
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, expand = c(0.02,0)
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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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msa_wt_logo_P = p1 +
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scale_y_continuous(expand = c(0,0.09)) +
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scale_x_discrete(breaks = i2_extract
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, expand = c(0.09,0)
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, expand = c(x_axis_offset, 0)
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, labels = i2_extract
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, limits = factor(i2_extract))
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}
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cat('\nDone: msa_wt_logo_P')
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cat('\nDone: MSA plot for WT')
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#return(msa_wt_logoP)
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LogoPlotMSAL[['msa_wt_logoP']] <- msa_wt_logo_P
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