refactoring logo plots to add flame bar
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4 changed files with 194 additions and 196 deletions
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@ -46,7 +46,7 @@ LogoPlotCustomH <- function(plot_df
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, rm_empty_y = F
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, y_axis_log = F
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, log_value = log10
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, y_axis_increment = 5
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, y_axis_increment = 50
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, x_lab = "Position"
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, y_lab = "Odds Ratio"
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, x_ats = 12 # text size
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@ -68,16 +68,24 @@ LogoPlotCustomH <- function(plot_df
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#################################
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# Data processing for logo plot
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#################################
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plot_df = generate_distance_colour_map(plot_df, yvar_colname = y_axis_colname, debug=TRUE)
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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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if (rm_empty_y){
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plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
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cat("\nRemoving empty positions...\n")
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}else{
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plot_df = plot_df
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}
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y_max = max(plot_df['or_mychisq'], na.rm = T)
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y_max = max(plot_df[[y_axis_colname]], na.rm = T)
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cat("\nRemoving y scale incremenet:", y_axis_increment)
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y_lim = round_any(y_max, y_axis_increment, f = ceiling)
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@ -155,50 +163,90 @@ LogoPlotCustomH <- function(plot_df
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y_lab = paste("Log", y_lab)
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}
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}
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ggseqlogo(logo_dfP_wf
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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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#ylab("my custom height") +
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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_text(size = y_ats
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, angle = y_tangle
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plot_grid(
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ggplot() +
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geom_logo(logo_dfP_wf
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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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#ylab("my custom height") +
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theme( axis.ticks.x = element_blank()
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, axis.title.x = element_blank()
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, axis.text.x = element_blank() # turn this off and the below on if you want to visually
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# verify positions.
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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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# , margin = margin(b=0)
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# )
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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 = 0
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, colour = yfont_bgc)
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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.text = element_blank()
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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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, plot.margin = margin(b=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
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#, breaks
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, labels = position_or
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, limits = factor(1:length(position_or))) +
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scale_y_continuous(y_lab
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, breaks = seq(0, (y_lim), by = y_axis_increment)
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#, labels = seq(0, (y_lim), by = y_axis_increment)
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, limits = c(0, y_lim)) +
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labs(y=y_lab),
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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
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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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, 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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scale_x_discrete(x_lab
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#, breaks
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, labels = position_or
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, limits = factor(1:length(position_or))) +
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scale_y_continuous(y_lab
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, breaks = seq(0, (y_lim), by = y_axis_increment)
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#, labels = seq(0, (y_lim), by = y_axis_increment)
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, limits = c(0, y_lim)) +
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ylab(y_lab) +
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geom_tile(aes(plot_df$position, tpos0 # heat-mapped distance tiles along the bot
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, width = tW0
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, height = tH0)
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, fill = plot_df$ligD_colours
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, colour = plot_df$ligD_colours
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, linetype = "blank")
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#LogoPlot = p0 + ylab(y_lab)
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#return(LogoPlot)
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}
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, vjust = 0.4
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, colour = xfont_bgc)
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, axis.text.y = element_blank()
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, axis.ticks.y = element_blank()
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, axis.title.x = element_text(size = x_tts
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, colour = xtt_col)
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, legend.title = element_text(size = leg_tts
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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, legend.position = leg_pos
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, legend.direction = leg_dir
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, plot.background = element_rect(fill = theme_bgc)
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, plot.margin = margin(t=0)
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, panel.grid=element_blank()
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, panel.background = element_rect(fill = theme_bgc)
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) +
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scale_x_discrete(x_lab, labels=factor(unique_colour_map$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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ncol=1, align='v', rel_heights = c(8/10,1/10)
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)
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}
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#LogoPlotCustomH(merged_df3)
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