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cd9b1ad245
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10 changed files with 208 additions and 128 deletions
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@ -36,10 +36,10 @@ ColourPalleteMulti = function(df, group, subgroup){
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bp_stability_hmap <- function(plot_df = merged_df3
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, xvar_colname = "position"
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, yvar_colname = 'duet_scaled' # Only here so that you can do function(df)
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, yvar_colname = 'avg_stability_scaled' # Only here so that you can do function(df)
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#, bar_col_colname = "group"
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, stability_colname = "duet_scaled" # Only here so that you can do function(df)
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, stability_outcome_colname = "duet_outcome" # Only here so that you can do function(df)
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, stability_colname = "avg_stability_scaled" # Only here so that you can do function(df)
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, stability_outcome_colname = "avg_stability_outcome" # Only here so that you can do function(df)
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, p_title = "DUMMY TITLE", # Only here so that you can do function(df)
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my_xaxls = 6, # x-axis label size
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my_yaxls = 6, # y-axis label size
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@ -54,15 +54,18 @@ bp_stability_hmap <- function(plot_df = merged_df3
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, lig_dist_colname = LigDist_colname # from globals
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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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, tH0 = 0.2,
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y_max_override = 1, # an override for tidily plotting multiple different-ranged plots together
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reorder_position = FALSE # enable to reorder according to plot_df$pos_count
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)
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{
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# Custom 2: x-axis geom tiles ~ lig distance
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# order the df by position and ensure it is a factor
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# order the df by position and ensure it is a factor
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plot_df = plot_df[order(plot_df[[xvar_colname]]), ]
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plot_df[[xvar_colname]] = factor(plot_df[[xvar_colname]])
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@ -76,10 +79,18 @@ bp_stability_hmap <- function(plot_df = merged_df3
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#
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# Add col: 'group'
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plot_df$group = paste0(plot_df[[stability_outcome_colname]], "_", my_grp, sep = "")
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plot_df=plot_df %>% dplyr::add_count(position)
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plot_df$pos_count=plot_df$n
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plot_df$n=NULL
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# check unique values in normalised data
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# cat("\nNo. of unique values in", stability_colname, "no rounding:"
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# , length(unique(plot_df[[stability_colname]])))
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# define a "max Y" in case the user didn't supply one
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if(reorder_position) {
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y_max = max(plot_df$pos_count)
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}
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else{
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y_max = 1 # boring default
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}
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y_axis_limit = round_any(y_max, y_max_override, ceiling)
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# Call the function to create the palette based on the group defined above
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#subcols_ps
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@ -87,55 +98,63 @@ bp_stability_hmap <- function(plot_df = merged_df3
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cat("\nNo. of sub colours generated:", length(subcols_bp_hmap))
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anno_bar=position_annotation(plot_df,
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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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reorder_position=reorder_position,
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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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)
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# Generate the subcols barplot
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cowplot::plot_grid(
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ggplot(plot_df, aes_string(x = xvar_colname
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#, ordered = T
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)
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) +
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geom_bar(aes(fill = group)
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, colour = "grey", size=0.125) +
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scale_fill_manual( values = subcols_bp_hmap
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, guide = "none") +
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# scale_x_discrete("Position", labels=factor(plot_df$position)) +
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theme(
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panel.grid = element_line(color="lightgrey", size=0.125)
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, axis.text.x = element_text(size = my_xaxls
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subcols_plot = ggplot(plot_df) +
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scale_fill_manual( values = subcols_bp_hmap
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, guide = "none") +
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# scale_x_discrete("Position", labels=factor(plot_df$position)) +
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scale_y_continuous(limits=c(0,y_axis_limit)) +
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theme(
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panel.grid = element_line(color="lightgrey", size=0.125)
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, axis.text.x = element_text(size = my_xaxls
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, angle = 90
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, hjust = 1
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, vjust = 0.4)
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, axis.text.y = element_text(size = my_yaxls
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_blank()
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, axis.ticks = element_blank()
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#, axis.title.x = element_text(size = my_xaxts)
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, axis.title.y = element_text(size = my_yaxts )
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, plot.title = element_text(size = my_pts
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, hjust = 0.5)
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# , panel.grid = element_blank()
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, panel.background = element_rect(fill = "transparent", colour=NA)
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) +
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labs(title = p_title
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, x = my_xlab
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, y = my_ylab),
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, axis.text.y = element_text(size = my_yaxls
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_blank()
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, axis.ticks = element_blank()
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#, axis.title.x = element_text(size = my_xaxts)
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, axis.title.y = element_text(size = my_yaxts )
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, plot.title = element_text(size = my_pts
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, hjust = 0.5)
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# , panel.grid = element_blank()
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, panel.background = element_rect(fill = "transparent", colour=NA)
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) +
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labs(title = p_title
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, x = my_xlab
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, y = my_ylab) +
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if(reorder_position) {
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geom_bar(aes(x=reorder(position,-pos_count), fill = group),
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colour = "grey",
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size=0.125
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)
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}else{
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geom_bar(aes(x=position, fill = group),
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colour = "grey",
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size=0.125
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)
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}
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# Generate the subcols barplot
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cowplot::plot_grid(
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subcols_plot,
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NULL,
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anno_bar,
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#generate_distance_legend(plot_df),
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ncol = 1,
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align = "v",
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rel_heights = c(6,-0.1,1)
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#rel_widths = c(9/10, 0.4/10)
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)
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}
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