added my_logolas.R
This commit is contained in:
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5 changed files with 1423 additions and 93 deletions
19
config/gid.R
19
config/gid.R
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@ -2,7 +2,20 @@ gene = "gid"
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drug = "streptomycin"
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rna_bind_aa_pos = c(96, 97, 118, 163)
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bin_aa_pos = c(48, 51, 137, 200)
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active_aa_pos = c(rna_bind_aa_pos, bin_aa_pos)
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binding_aa_pos = c(48, 51, 137, 200)
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active_aa_pos = sort(unique(c(rna_bind_aa_pos, binding_aa_pos)))
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#rna_site = G518
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cat("\nNo. of active site residues for gene"
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, gene, ":"
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, length(active_aa_pos)
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, "\nThese are:\n"
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, active_aa_pos)
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cat("\n==================================================="
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, "\nActive site residues for", gene, "comprise of..."
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, "\n==================================================="
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, "\nRNA binding residues:"
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, rna_bind_aa_pos
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, "\nBinding site residues:"
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, binding_aa_pos)
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@ -1,2 +1,36 @@
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gene = "pncA"
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drug = "pyrazinamide"
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#===================================
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#Iron centre --> purple
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#Catalytic triad --> yellow
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#Substrate binding --> teal and blue
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#H-bond --> green
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#====================================
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metal_aa_pos = c(49, 51, 57, 71)
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catalytic_aa_pos = c(8, 96, 138)
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substrate_aa_pos = c(13, 68, 103, 137)
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hbond_aa_pos = c(133, 134, 8, 138)
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active_aa_pos = sort(unique(c(metal_aa_pos
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, catalytic_aa_pos
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, substrate_aa_pos
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, hbond_aa_pos)))
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cat("\nNo. of active site residues for gene"
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, gene, ":"
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, length(active_aa_pos)
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, "\nThese are:\n"
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, active_aa_pos)
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cat("\n==================================================="
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, "\nActive site residues for", gene, "comprise of..."
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, "\n==================================================="
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, "\nMetal coordination centre residues:"
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, metal_aa_pos
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, "\nCatalytic triad residues:"
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, catalytic_aa_pos
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, "\nSubstrate binding residues:"
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, substrate_aa_pos
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, "\nH-bonding residues:"
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, hbond_aa_pos)
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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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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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, "\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("\nAll positions within range"
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, "\nProceeing with generating requested position MSA seqs...")
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i_extract = plot_positions
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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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@ -92,40 +117,42 @@ 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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wt_interimDF = data.frame(wt_interim)
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wt_pos = as.numeric(rownames(wt_interimDF))
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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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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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@ -144,7 +171,8 @@ 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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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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@ -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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@ -238,19 +270,23 @@ 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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1225
scripts/functions/my_logolas.R
Normal file
1225
scripts/functions/my_logolas.R
Normal file
File diff suppressed because it is too large
Load diff
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@ -1,32 +1,29 @@
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#source("~/git/LSHTM_analysis/config/gid.R")
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#source("~/git/LSHTM_analysis/config/pnca.R") # YES
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source("~/git/LSHTM_analysis/config/embb.R")
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#---------------------------------------------------
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# FIXME
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# source("~/git/LSHTM_analysis/config/alr.R")
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# source("~/git/LSHTM_analysis/config/embb.R")
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# source("~/git/LSHTM_analysis/config/katg.R")
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# source("~/git/LSHTM_analysis/config/rpob.R")
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source("~/git/LSHTM_analysis/config/pnca.R") # YES
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#source("~/git/LSHTM_analysis/config/embb.R")
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#source("~/git/LSHTM_analysis/config/katg.R")
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#source("~/git/LSHTM_analysis/config/alr.R")
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#source("~/git/LSHTM_analysis/config/rpob.R")
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#---------------------------------------------------
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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#
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# ################################
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# # Logo plot with custom Y axis
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# # mainly OR
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# # script: logoP.R
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# ################################
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################################
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# Logo plot with custom Y axis
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# mainly OR
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# script: logoP.R
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################################
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# LogoPlotCustomH (plot_df = merged_df3
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# , x_axis_colname = "position"
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# , y_axis_colname = "or_mychisq"
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# , symbol_colname = "mutant_type"
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# , y_axis_log = F
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# , y_axis_log = T
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# , log_value = log10
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# , y_axis_increment = 5
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# , rm_empty_y = F
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# , y_axis_increment = 100
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# , rm_empty_y = T
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# , my_logo_col = 'chemistry'
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# , x_lab = "Wild-type position"
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# , y_lab = "Odds Ratio"
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# , x_ats = 12 # text size
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# , x_ats = 10 # text size
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# , x_tangle = 90 # text angle
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# , y_ats = 22
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# , y_tangle = 0
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@ -38,24 +35,24 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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# , leg_ts = 15 # 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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#
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# # ########################################
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# # # Logo plot showing nsSNPs by positions
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# # # wild-type and mutant aa
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# # # script: logoP_snp.R
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# # ########################################
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########################################
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# Logo plot showing nsSNPs by positions
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# wild-type and mutant aa
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# script: logoP_snp.R
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########################################
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# LogoPlotSnps(plot_df = merged_df3
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# , x_axis_colname = "position"
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# , symbol_mut_colname = "mutant_type"
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# , symbol_wt_colname = "wild_type"
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# , omit_snp_count = c(0)# can be 1, 2, etc.
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# , omit_snp_count = c(1)# can be 0,1, 2, etc.
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# , my_logo_col = "chemistry"
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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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# , y_lab = "nsSNP count"
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# , x_ats = 10 # text size
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# , x_tangle = 90 # text angle
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# , y_ats = 20
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# , y_ats = 18
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# , y_tangle = 0
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# , x_tts = 18 # title size
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# , y_tts = 18
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@ -65,7 +62,6 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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# , leg_tts = 16 # leg title size
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# )
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#
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#
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########################################
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# Logo plot MSA
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@ -76,21 +72,47 @@ source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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# To plot entire MSA, simply don't specify {plot_positions}
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# script: logoP_msa.R
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# TODO perhaps: ED logo from Logolas
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########################################
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# LogoPlotMSA(msaSeq_mut = msa_seq
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# , msaSeq_wt = wt_seq
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# , msa_method = 'bits' # or probability
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# , my_logo_col = "taylor"
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# , plot_positions = active_aa_pos
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# , x_lab = "nsSNP position"
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# , y_lab = ""
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# , x_ats = 10 # text size
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# , x_tangle = 90 # text angle
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# , x_axis_offset = 0.05
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# , y_ats = 15
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# , y_tangle = 0
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# , x_tts = 13 # title size
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# , y_tts = 15
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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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LogoPlotMSA(msaSeq_mut = msa_seq
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# ED Logo plot MSA
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# Mutant and wild-type
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########################################
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LogoPlotED(msaSeq_mut = msa_seq
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, msaSeq_wt = wt_seq
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, msa_method = 'bits' # or probability
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, my_logo_col = "taylor"
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#, plot_positions = c(24, 54, 48, 58, 44, 80, 87, 1000:1008)
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, plot_positions = active_aa_pos
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, x_lab = "nsSNP position"
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, y_lab = ""
|
||||
, x_ats = 10 # text size
|
||||
, x_tangle = 90 # text angle
|
||||
, y_ats = 13
|
||||
, x_axis_offset = 0.05
|
||||
, y_ats = 15
|
||||
, y_tangle = 0
|
||||
, x_tts = 13 # title size
|
||||
, y_tts = 13
|
||||
, y_tts = 15
|
||||
, leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
|
||||
, leg_dir = "horizontal" #can be vertical or horizontal
|
||||
, leg_ts = 16 # leg text size
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue