refactoring logo plots to add flame bar
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4 changed files with 194 additions and 196 deletions
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@ -33,7 +33,7 @@
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LogoPlotSnps <- function(plot_df
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, x_axis_colname = "position"
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, symbol_mut_colname = "mutant_type"
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, symbol_wt_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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, my_logo_col = "chemistry"
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, x_lab = "Position"
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@ -66,11 +66,18 @@ LogoPlotSnps <- function(plot_df
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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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#
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setDT(plot_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$mut_pos_occurrence)
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table(plot_df[[x_axis_colname]])
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table(plot_df$mut_pos_occurrence)
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}
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max_mut = max(table(plot_df[[x_axis_colname]]))
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@ -200,7 +207,7 @@ LogoPlotSnps <- function(plot_df
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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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@ -212,11 +219,7 @@ LogoPlotSnps <- function(plot_df
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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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theme(text=element_text(family="FreeSans"))+
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theme(axis.text.x = element_blank()) +
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theme_logo()+
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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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@ -224,16 +227,9 @@ LogoPlotSnps <- function(plot_df
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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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# FIXME: currently broken, possibly due to ggseqlogo() not working in the
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# way standard ggplot2() does
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geom_tile(aes(plot_df$position, tpos0 # heat-mapped distance tiles along the bottom.
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, width = tW0
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, height = tH0)
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, fill = plot_df$ligD_colours
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, colour = plot_df$ligD_colours
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, linetype = "blank") +
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ylab(y_lab) +
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theme(legend.position = leg_pos
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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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@ -260,40 +256,58 @@ LogoPlotSnps <- function(plot_df
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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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theme(text = element_text(family="FreeSans"))+
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theme(axis.text.x = element_blank()
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, axis.text.y = element_blank()) +
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theme_logo()+
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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 = colnames(tab_wt))+
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xlab(x_lab) +
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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 = y_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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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)
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) +
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labs(x=NULL, y=NULL)
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,
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ggplot(data=unique_colour_map2, 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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geom_tile() +
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theme(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_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)
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)
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, nrow = 2
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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)
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) +
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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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, nrow = 3
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, align = "v"
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, rel_heights = c(3/4, 1/4))
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, rel_heights = c(7/10, 2/7, 1/7))
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#------------------
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# Wild logo plot
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#------------------
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}
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#LogoPlotSnps(mutable_df3)
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