various usability tweaks to LogoPlotMSA and position_annotation
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4 changed files with 197 additions and 130 deletions
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@ -4,6 +4,7 @@
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position_annotation=function(plot_df,
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bg="transparent",
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reorder_position = FALSE, # enable to reorder according to plot_df$pos_count
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generate_colours = TRUE, #set FALSE if you want to generate all the colour columns elsewhere
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aa_pos_drug=1:100,
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active_aa_pos=1:100,
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aa_pos_lig1=1:100,
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@ -32,36 +33,38 @@ position_annotation=function(plot_df,
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#plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
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# plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
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# "brown", "transparent")
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plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
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"transparent", "transparent")
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plot_df$bg_all = plot_df$col_aa
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plot_df$bg_all = ifelse(plot_df[["position"]]%in%aa_pos_drug,
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"drug", plot_df$bg_all)
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plot_df$col_bg1 = plot_df$bg_all
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plot_df$col_bg1 = ifelse(plot_df[["position"]]%in%aa_pos_lig1,
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"lig1", plot_df$col_bg1)
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plot_df$col_bg2 = plot_df$col_bg1
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plot_df$col_bg2 = ifelse(plot_df[["position"]]%in%aa_pos_lig2,
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"lig2", plot_df$col_bg2)
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plot_df$col_bg3 = plot_df$col_bg2
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plot_df$col_bg3 = ifelse(plot_df[["position"]]%in%aa_pos_lig3
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, "lig3", plot_df$col_bg3)
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# the call to generate_distance_colour_map should probably be
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# wherever the outer DF is built, and not here.
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plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
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if (generate_colours){
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plot_df$col_aa = ifelse(plot_df[["position"]]%in%active_aa_pos,
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"transparent", "transparent")
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plot_df$bg_all = plot_df$col_aa
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plot_df$bg_all = ifelse(plot_df[["position"]]%in%aa_pos_drug,
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"drug", plot_df$bg_all)
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plot_df$col_bg1 = plot_df$bg_all
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plot_df$col_bg1 = ifelse(plot_df[["position"]]%in%aa_pos_lig1,
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"lig1", plot_df$col_bg1)
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plot_df$col_bg2 = plot_df$col_bg1
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plot_df$col_bg2 = ifelse(plot_df[["position"]]%in%aa_pos_lig2,
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"lig2", plot_df$col_bg2)
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plot_df$col_bg3 = plot_df$col_bg2
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plot_df$col_bg3 = ifelse(plot_df[["position"]]%in%aa_pos_lig3
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, "lig3", plot_df$col_bg3)
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# the call to generate_distance_colour_map should probably be
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# wherever the outer DF is built, and not here.
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plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
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}
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heat_bar = ggplot(plot_df) + # THIS STUPID FUCKING FACTOR THING
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# scale_x_discrete("Position", labels=factor(plot_df$position)) +
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theme_nothing() +
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theme(#axis.text.x = element_text(angle = 90, size = 6),
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title = element_blank()
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title = element_blank()
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) + # enable for alignment debug
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labs(x = NULL, y = NULL) +
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@ -77,87 +80,87 @@ position_annotation=function(plot_df,
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}
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#end of distance-heat-bar
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#NULL,
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if(reorder_position) {
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pos_tiles = ggplot(plot_df) +
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#scale_x_discrete("Position", labels=factor(plot_df$position)) +
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scale_color_manual(values = c(
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"brown"="brown",
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"drug"=drug_colour,
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"transparent"="transparent",
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"lig1"=lig1_colour,
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"lig2"=lig2_colour,
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"lig3"=lig3_colour
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),
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#expand=c(0,0)
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) +
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scale_fill_manual(values = c(
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"brown"="brown",
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"drug"=drug_colour,
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"transparent"="transparent",
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"lig1"=lig1_colour,
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"lig2"=lig2_colour,
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"lig3"=lig3_colour
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),
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#expand=c(0,0)
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) +
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theme_nothing() +
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theme(plot.background = element_rect(fill = bg, colour=NA),
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#plot.margin = margin(t=0,b=0),
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panel.background = element_rect(fill = bg, colour=NA),
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legend.position = "none"
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) +
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labs(x = NULL, y= NULL) +
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if(reorder_position) {
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pos_tiles = ggplot(plot_df) +
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#scale_x_discrete("Position", labels=factor(plot_df$position)) +
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scale_color_manual(values = c(
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"brown"="brown",
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"drug"=drug_colour,
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"transparent"="transparent",
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"lig1"=lig1_colour,
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"lig2"=lig2_colour,
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"lig3"=lig3_colour
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),
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#expand=c(0,0)
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) +
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scale_fill_manual(values = c(
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"brown"="brown",
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"drug"=drug_colour,
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"transparent"="transparent",
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"lig1"=lig1_colour,
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"lig2"=lig2_colour,
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"lig3"=lig3_colour
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),
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#expand=c(0,0)
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) +
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theme_nothing() +
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theme(plot.background = element_rect(fill = bg, colour=NA),
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#plot.margin = margin(t=0,b=0),
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panel.background = element_rect(fill = bg, colour=NA),
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legend.position = "none"
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) +
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labs(x = NULL, y= NULL) +
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geom_tile(aes(y = 1,x=reorder(position,-pos_count), fill = bg_all, colour = bg_all)
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) +
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geom_tile(aes(y = 2, x=reorder(position,-pos_count), fill = col_bg1, colour = col_bg1)
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) +
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geom_tile(aes(y = 3, x=reorder(position,-pos_count), fill = col_bg2, colour = col_bg2)
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) +
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geom_tile(aes(y = 4, x=reorder(position,-pos_count), fill = col_bg3, colour = col_bg3)
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)
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} else {
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pos_tiles = ggplot(plot_df) +
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#scale_x_discrete("Position", labels=factor(plot_df$position)) +
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scale_color_manual(values = c(
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"brown"="brown",
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"drug"=drug_colour,
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"transparent"="transparent",
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"lig1"=lig1_colour,
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"lig2"=lig2_colour,
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"lig3"=lig3_colour
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),
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#expand=c(0,0)
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) +
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scale_fill_manual(values = c(
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"brown"="brown",
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"drug"=drug_colour,
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"transparent"="transparent",
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"lig1"=lig1_colour,
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"lig2"=lig2_colour,
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"lig3"=lig3_colour
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),
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#expand=c(0,0)
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) +
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theme_nothing() +
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theme(plot.background = element_rect(fill = bg, colour=NA),
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#plot.margin = margin(t=0,b=0),
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panel.background = element_rect(fill = bg, colour=NA),
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legend.position = "none"
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) +
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labs(x = NULL, y= NULL) +
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geom_tile(aes(y = 2, x=reorder(position,-pos_count), fill = col_bg1, colour = col_bg1)
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) +
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geom_tile(aes(y = 3, x=reorder(position,-pos_count), fill = col_bg2, colour = col_bg2)
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) +
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geom_tile(aes(y = 4, x=reorder(position,-pos_count), fill = col_bg3, colour = col_bg3)
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)
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} else {
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pos_tiles = ggplot(plot_df) +
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#scale_x_discrete("Position", labels=factor(plot_df$position)) +
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scale_color_manual(values = c(
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"brown"="brown",
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"drug"=drug_colour,
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"transparent"="transparent",
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"lig1"=lig1_colour,
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"lig2"=lig2_colour,
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"lig3"=lig3_colour
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),
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#expand=c(0,0)
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) +
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scale_fill_manual(values = c(
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"brown"="brown",
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"drug"=drug_colour,
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"transparent"="transparent",
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"lig1"=lig1_colour,
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"lig2"=lig2_colour,
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"lig3"=lig3_colour
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),
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#expand=c(0,0)
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) +
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theme_nothing() +
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theme(plot.background = element_rect(fill = bg, colour=NA),
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#plot.margin = margin(t=0,b=0),
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panel.background = element_rect(fill = bg, colour=NA),
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legend.position = "none"
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) +
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labs(x = NULL, y= NULL) +
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geom_tile(aes(y = 1, x=factor(position), fill = bg_all, colour = bg_all)
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) +
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geom_tile(aes(y = 2, x=factor(position), fill = col_bg1, colour = col_bg1)
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) +
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geom_tile(aes(y = 3, x=factor(position), fill = col_bg2, colour = col_bg2)
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) +
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geom_tile(aes(y = 4, x=factor(position), fill = col_bg3, colour = col_bg3)
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)
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}
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# tile thingies end
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heat_legend=get_legend(heat_bar)
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geom_tile(aes(y = 2, x=factor(position), fill = col_bg1, colour = col_bg1)
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) +
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geom_tile(aes(y = 3, x=factor(position), fill = col_bg2, colour = col_bg2)
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) +
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geom_tile(aes(y = 4, x=factor(position), fill = col_bg3, colour = col_bg3)
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)
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}
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# tile thingies end
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heat_legend=get_legend(heat_bar)
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out_plot=cowplot::plot_grid(
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heat_bar,
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NULL,
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