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10 changed files with 833 additions and 285 deletions
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@ -1,7 +1,7 @@
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########################a###########################################################
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# Input:
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# Data
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# plot_df: merged_df3 containing the OR column to use as y-axis or any other relevant column
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# mutable_df: merged_df3 containing the OR column to use as y-axis or any other relevant column
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# x_axis_colname = "position"
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# symbol_mut_colname = "mutant_type"
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@ -38,16 +38,16 @@ LogoPlotSnps <- function(plot_df
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, my_logo_col = "chemistry"
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, x_lab = "Position"
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, y_lab = "Count"
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, x_ats = 14 # text size
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, x_ats = 7 # text size
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, x_tangle = 90 # text angle
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, y_ats = 22
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, y_ats = 10
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, y_tangle = 0
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, x_tts = 20 # title size
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, y_tts = 23
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, x_tts = 10 # title size
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, y_tts = 10
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, leg_pos = "none" # 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 = 20 # leg text size
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, leg_tts = 16 # leg title size
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, leg_ts = 10 # leg text size
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, leg_tts = 8 # leg title size
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, tpos0 = 0 # 0 is a magic number that does my sensible default
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, tW0 = 1
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, tH0 = 0.2
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@ -56,6 +56,7 @@ LogoPlotSnps <- function(plot_df
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)
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{
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mutable_df=cbind(plot_df)
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# handle funky omit_snp_count. DOES NOT WORK YET
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if (class(omit_snp_count) != "numeric"){
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omit_snp_count <- as.numeric(unlist(str_extract_all(omit_snp_count, regex("[0-9]+"))))
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@ -65,51 +66,51 @@ LogoPlotSnps <- function(plot_df
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############################################
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# Generate "ligand distance" colour map
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plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
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unique_colour_map = unique(plot_df[,c("position","ligD_colours")])
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unique_colour_map = unique_colour_map[order(unique_colour_map$position), ]
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rownames(unique_colour_map) = unique_colour_map$position
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unique_colour_map2 = unique_colour_map
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unique_colour_map2$position=as.factor(unique_colour_map2$position)
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unique_colour_map2$ligD_colours = as.factor(unique_colour_map2$ligD_colours)
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# mutable_df = generate_distance_colour_map(mutable_df, debug=TRUE)
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# unique_colour_map = unique(mutable_df[,c("position","ligD_colours")])
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# unique_colour_map = unique_colour_map[order(unique_colour_map$position), ]
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# rownames(unique_colour_map) = unique_colour_map$position
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# unique_colour_map2 = unique_colour_map
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# unique_colour_map2$position=as.factor(unique_colour_map2$position)
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# unique_colour_map2$ligD_colours = as.factor(unique_colour_map2$ligD_colours)
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#
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setDT(plot_df)[, mut_pos_occurrence := .N, by = .(eval(parse(text=x_axis_colname)))]
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setDT(mutable_df)[, mut_pos_occurrence := .N, by = .(eval(parse(text=x_axis_colname)))]
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if (debug) {
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table(plot_df[[x_axis_colname]])
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table(plot_df$mut_pos_occurrence)
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table(mutable_df[[x_axis_colname]])
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table(mutable_df$mut_pos_occurrence)
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}
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max_mut = max(table(plot_df[[x_axis_colname]]))
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max_mut = max(table(mutable_df[[x_axis_colname]]))
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# Subset Data as specified by user
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cat("\nDisplaying nsSNP position frequency:\n")
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print(table(plot_df$mut_pos_occurrence))
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print(table(mutable_df$mut_pos_occurrence))
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if ( (length(omit_snp_count) ==1) && (omit_snp_count == 0) ){
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my_data_snp = plot_df
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my_data_snp = mutable_df
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u = unique(my_data_snp[[x_axis_colname]])
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max_mult_mut = max(table(my_data_snp[[x_axis_colname]]))
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if (debug) {
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cat("\nNo filtering requested:"
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, "\nTotal no. of nsSNPs:", sum(table(plot_df$mut_pos_occurrence))
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, "\nTotal no. of nsSNPs omitted:", sum(table(plot_df$mut_pos_occurrence)[omit_snp_count])
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, "\nTotal no. of nsSNPs:", sum(table(mutable_df$mut_pos_occurrence))
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, "\nTotal no. of nsSNPs omitted:", sum(table(mutable_df$mut_pos_occurrence)[omit_snp_count])
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, "\nDim of data:", dim(my_data_snp)
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, "\nNo. of positions:", length(u)
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, "\nMax no. of muts at any position:", max_mult_mut)
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}
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} else {
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my_data_snp = subset(plot_df, !(mut_pos_occurrence%in%omit_snp_count) )
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my_data_snp = subset(mutable_df, !(mut_pos_occurrence%in%omit_snp_count) )
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exp_nrows = sum(table(plot_df$mut_pos_occurrence)) - sum(table(plot_df$mut_pos_occurrence)[omit_snp_count])
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exp_nrows = sum(table(mutable_df$mut_pos_occurrence)) - sum(table(mutable_df$mut_pos_occurrence)[omit_snp_count])
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got_rows = sum(table(my_data_snp$mut_pos_occurrence))
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u = unique(my_data_snp[[x_axis_colname]])
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max_mult_mut = max(table(my_data_snp[[x_axis_colname]]))
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if (debug) {
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if (got_rows == exp_nrows) {
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cat("\nPass: Position with the stated nsSNP frequency filtered:", omit_snp_count
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, "\nTotal no. of nsSNPs:", sum(table(plot_df$mut_pos_occurrence))
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, "\nTotal no. of nsSNPs omitted:", sum(table(plot_df$mut_pos_occurrence)[omit_snp_count])
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, "\nTotal no. of nsSNPs:", sum(table(mutable_df$mut_pos_occurrence))
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, "\nTotal no. of nsSNPs omitted:", sum(table(mutable_df$mut_pos_occurrence)[omit_snp_count])
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, "\nDim of subsetted data:", dim(my_data_snp)
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, "\nNo. of positions:", length(u)
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, "\nMax no. of muts at any position:", max_mult_mut)
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@ -145,7 +146,7 @@ LogoPlotSnps <- function(plot_df
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if (is.matrix(tab_mt)){
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if (debug) {
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cat("\nCreating mutant matrix..."
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#, "\nRownames of mutant matrix:", rownames(tab_mt)
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#, "\nRowna mes of mutant matrix:", rownames(tab_mt)
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#, "\nColnames of mutant matrix:", colnames(tab_mt)
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)
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}
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@ -211,114 +212,95 @@ LogoPlotSnps <- function(plot_df
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#####################################
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# Generating logo plots for nsSNPs
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#####################################
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cowplot::plot_grid(
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#-------------------
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# Mutant logo plot
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#-------------------
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ggseqlogo(tab_mt
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, method = 'custom'
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, col_scheme = my_logo_col
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, seq_type = 'aa') +
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scale_x_continuous(breaks = 1:ncol(tab_mt)
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, expand = c(0.01,0)
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, labels = colnames(tab_mt))+
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scale_y_continuous(breaks = 0:(max_mult_mut-1)
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, labels = c(1:max_mult_mut)
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, limits = c(0, max_mult_mut)) +
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ylab(y_lab) +
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theme(text=element_text(family="FreeSans")
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, legend.position = leg_pos
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, legend.direction = leg_dir
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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_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, colour=NA)
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),
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ggseqlogo(tab_wt
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, method = 'custom'
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, col_scheme = my_logo_col
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, seq_type = 'aa') +
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scale_x_continuous(breaks = 1:ncol(tab_wt)
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, expand = c(0.01,0)
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, labels = as.factor(colnames(tab_wt))) +
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theme(text = element_text(family="FreeSans")
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, legend.position = "none"
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, axis.text.x = element_blank()
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, axis.text.y = element_blank()
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, axis.title.x = element_blank()
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, axis.title.y = element_blank()
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, plot.background = element_rect(fill = theme_bgc, colour=NA)
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) +
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labs(x=NULL, y=NULL),
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ggplot(
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data=unique_colour_map2,
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aes(
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x=factor(position), 0 # heat-mapped distance tiles along the bot
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, fill = position
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, colour = position
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, linetype = "blank"
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)
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#-------------------
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# Mutant logo plot
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#-------------------
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logo_top =ggseqlogo(tab_mt
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, method = 'custom'
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, col_scheme = my_logo_col
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, seq_type = 'aa') +
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scale_x_continuous(breaks = 1:ncol(tab_mt)
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, expand = c(0.01,0)
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, labels = colnames(tab_mt))+
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scale_y_continuous(breaks = 0:(max_mult_mut-1)
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, labels = c(1:max_mult_mut)
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, limits = c(0, max_mult_mut)) +
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ylab(y_lab) +
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theme(text=element_text(family="FreeSans")
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, legend.position = leg_pos
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, legend.direction = leg_dir
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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_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.x = element_blank()
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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, colour=NA)
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)
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logo_bottom = ggseqlogo(tab_wt
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, method = 'custom'
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, col_scheme = my_logo_col
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, seq_type = 'aa') +
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scale_x_continuous(breaks = 1:ncol(tab_wt)
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, expand = c(0.01,0)
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, labels = as.factor(colnames(tab_wt))) +
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theme(text = element_text(family="FreeSans")
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, legend.position = "none"
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, axis.text.x = element_blank()
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, axis.text.y = element_blank()
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, axis.title.x = element_blank()
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, axis.title.y = element_blank()
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, plot.background = element_rect(fill = theme_bgc, colour=NA)
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) +
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geom_tile() +
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theme(
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axis.text.x = element_blank()
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, axis.ticks.x = element_blank()
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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.ticks.y = element_blank()
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, axis.title.x = 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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# , 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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, legend.position = leg_pos
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, legend.direction = leg_dir
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, plot.background = element_rect(fill = theme_bgc, colour=NA)
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, plot.margin = margin(t=0)
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, panel.grid=element_blank()
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, panel.background = element_rect(fill = theme_bgc, colour=NA)
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) +
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scale_x_discrete(x_lab, labels=unique_colour_map$position) +
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#scale_x_discrete(x_lab, labels=factor(unique_colour_map$position)) +
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scale_color_manual(values=unique_colour_map$ligD_colours) +
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scale_fill_manual(values=unique_colour_map$ligD_colours) +
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labs(y = NULL)
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, NULL
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, position_annotation(plot_df, bg=theme_bgc)
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, ncol=1
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, align = "v"
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, axis='lr'
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, rel_heights = c(7/10, 2/7,1/7, -0.1, 0.5/7))
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labs(x=NULL, y=NULL)
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anno_bar = position_annotation(plot_df,
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bg = theme_bgc,
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aa_pos_drug=aa_pos_drug,
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active_aa_pos=active_aa_pos,
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aa_pos_lig1=aa_pos_lig1,
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aa_pos_lig2=aa_pos_lig2,
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aa_pos_lig3=aa_pos_lig3)
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aligned=align_plots(logo_top, logo_bottom, anno_bar, align='v', axis='lr')
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cowplot::plot_grid(
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aligned[[1]], aligned[[2]], aligned[[3]],
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ncol=1,
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#align = "v",
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rel_heights = c(7, 1,1),
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rel_widths = c(1,1,0.75)
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)
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# cowplot::plot_grid(
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# logo_top,
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# #NULL,
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# logo_bottom,
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# #NULL,
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# anno_bar,
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# ncol=1,
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# align = "v",
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# rel_heights = c(7, 1,1)
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# )
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# top logo, bottom logo, heat bar, NULL, position annotation
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#------------------
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# Wild logo plot
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#------------------
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}
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#LogoPlotSnps(small_df3)
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#LogoPlotSnps(mutable_df3)
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