various heat-bar/position tile faff
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4 changed files with 140 additions and 48 deletions
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@ -2,7 +2,7 @@
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# 1b: Define function: coloured barplot by subgroup
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# 1b: Define function: coloured barplot by subgroup
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# LINK: https://stackoverflow.com/questions/49818271/stacked-barplot-with-colour-gradients-for-each-bar
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# LINK: https://stackoverflow.com/questions/49818271/stacked-barplot-with-colour-gradients-for-each-bar
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#########################################################
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#########################################################
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source("~/git/LSHTM_analysis/scripts/functions/generate_distance_colour_map.R")
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#source("~/git/LSHTM_analysis/scripts/functions/generate_distance_colour_map.R")
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ColourPalleteMulti = function(df, group, subgroup){
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ColourPalleteMulti = function(df, group, subgroup){
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@ -121,16 +121,16 @@ bp_stability_hmap <- function(plotdf = merged_df3
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, axis.title.y = element_text(size = my_yaxts )
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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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, plot.title = element_text(size = my_pts
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, hjust = 0.5)) +
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, hjust = 0.5)) +
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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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geom_tile(aes(, tpos0 # heat-mapped distance tiles along the bot
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geom_tile(aes(, tpos0 # heat-mapped distance tiles along the bot
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, width = tW0
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, width = tW0
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, height = tH0)
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, height = tH0)
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, fill = plotdf$ligD_colours
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, fill = plotdf$ligD_colours
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, colour = plotdf$ligD_colours
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, colour = plotdf$ligD_colours
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, linetype = "blank") +
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, linetype = "blank"), #end of distance-heat-bar
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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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generate_distance_legend(plotdf),
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generate_distance_legend(plotdf),
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ncol = 2,
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ncol = 2,
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#align = "hv",
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#align = "hv",
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@ -171,20 +171,18 @@ LogoPlotCustomH <- function(plot_df
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, seq_type = "aa") +
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, seq_type = "aa") +
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#ylab("my custom height") +
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#ylab("my custom height") +
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theme( axis.ticks.x = element_blank()
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theme( axis.ticks.x = element_blank()
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, axis.ticks.length = unit(0, "pt")
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, axis.title.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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# , 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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# verify positions.
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# , axis.text.x = element_text(size = x_ats
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, axis.text.x = element_text(size = x_ats
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# , angle = x_tangle
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, angle = x_tangle
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# , hjust = 1
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, colour = xfont_bgc
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# , vjust = 0.4
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, vjust = 0.4
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# , colour = xfont_bgc
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, margin = margin(t=-8,r=0,b=0,l=0, unit="mm")
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# , margin = margin(b=0)
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)
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# )
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, axis.text.y = element_text(size = y_ats
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, axis.text.y = element_text(size = y_ats
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, angle = y_tangle
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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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, colour = yfont_bgc)
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, axis.title.y = element_text(size = y_tts
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, colour = ytt_col)
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@ -195,10 +193,11 @@ LogoPlotCustomH <- function(plot_df
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, legend.position = leg_pos
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, legend.position = leg_pos
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, legend.direction = leg_dir
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, legend.direction = leg_dir
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, plot.background = element_rect(fill = theme_bgc)
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#, plot.background = element_blank()
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, plot.margin = margin(b=0)
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, plot.margin = margin(b=0)
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, panel.grid=element_blank()
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, panel.grid=element_blank()
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, panel.background = element_rect(fill = theme_bgc)
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, plot.background = element_rect(fill = theme_bgc, colour=NA)
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, panel.background = element_rect(fill = "transparent", colour=NA)
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)+
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)+
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@ -220,15 +219,17 @@ LogoPlotCustomH <- function(plot_df
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)
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)
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) +
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) +
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geom_tile() +
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geom_tile() +
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theme(axis.text.x = element_text(size = x_ats
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theme(
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, angle = x_tangle
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axis.text.x = element_blank()
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, hjust = 1
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# axis.text.x = element_text(size = x_ats
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, vjust = 0.4
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# , angle = x_tangle
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, colour = xfont_bgc)
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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.text.y = element_blank()
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, axis.ticks.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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, axis.ticks.x = element_blank()
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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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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, colour = ytt_col)
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, legend.title = element_text(size = leg_tts
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, legend.title = element_text(size = leg_tts
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@ -237,16 +238,21 @@ LogoPlotCustomH <- function(plot_df
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, legend.position = leg_pos
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, legend.position = leg_pos
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, legend.direction = leg_dir
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, legend.direction = leg_dir
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, plot.background = element_rect(fill = theme_bgc)
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#, plot.background = element_blank()
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, plot.margin = margin(t=0)
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, plot.margin = margin(t=0,b=0)
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, panel.grid=element_blank()
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, panel.grid=element_blank()
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, panel.background = element_rect(fill = theme_bgc)
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, plot.background = element_rect(fill = theme_bgc, colour=NA)
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, panel.background = element_rect(fill = "transparent", colour=NA)
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#, panel.background = element_rect(fill = theme_bgc)
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#, panel.background = element_blank()
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) +
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) +
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scale_x_discrete(x_lab, labels=factor(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$ligD_colours) +
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scale_color_manual(values=unique_colour_map$ligD_colours) +
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scale_fill_manual(values=unique_colour_map$ligD_colours) +
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scale_fill_manual(values=unique_colour_map$ligD_colours) +
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labs(y = NULL),
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labs(y = NULL), NULL,
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ncol=1, align='v', rel_heights = c(8/10,1/10)
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position_annotation(plot_df, bg=theme_bgc),
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ncol=1, align='v', rel_heights = c(16,1,-0.1, 1)
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)
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)
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}
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}
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#LogoPlotCustomH(merged_df3)
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#LogoPlotCustomH(small_df3)
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27
scripts/minimal-heat-line-example.R
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27
scripts/minimal-heat-line-example.R
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@ -0,0 +1,27 @@
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#minimal example
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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 = 0.3
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plot_df = generate_distance_colour_map(plot_df, yvar_colname = stability_colname, debug=TRUE)
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cowplot::plot_grid(
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your_working_ggpot_statement + geom_tile(aes(, 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 = plotdf$ligD_colours
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, colour = plotdf$ligD_colours
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, linetype = "blank") +
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,
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generate_distance_legend(plot_df, yvar_colname = stability_colname)
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ncol = 2,
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#align = "hv",
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rel_widths = c(9/10, 0.4/10)
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)
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59
scripts/plotting/position_annotation.R
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59
scripts/plotting/position_annotation.R
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@ -0,0 +1,59 @@
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# position_annotation takes a Data Frame (df) and returns a ggplot object.
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#
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# This plots position tiles for the (up to) three ligands as well as drug
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position_annotation=function(plot_df, bg="transparent"){
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x_ats = 12
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x_tangle = 90
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x_tts = 20
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y_tts = 23
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xtt_col = "black"
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ytt_col = "black"
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leg_dir = "horizontal"
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leg_ts = 15
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leg_tts = 16
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leg_pos = "none"
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#plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
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ggplot(plot_df,
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aes(x=factor(position), # THIS STUPID FUCKING FACTOR THING
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)
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) +
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geom_tile(aes(y=0, fill= bg_all, colour = bg_all)
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) +
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geom_tile(aes(y=1, fill= col_bg1, colour = col_bg1)
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) +
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geom_tile(aes(y=2, fill= col_bg2, colour = col_bg2)
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) +
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geom_tile(aes(y=3, fill= col_bg3, colour = col_bg3)
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) +
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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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"purple"="purple",
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"transparent"="transparent",
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"blue"="blue", "cyan"="cyan",
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"cornflowerblue"="cornflowerblue"
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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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"purple"="purple",
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"transparent"="transparent",
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"blue"="blue",
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"cyan"="cyan",
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"cornflowerblue"="cornflowerblue"
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),
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expand=c(0,0)
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) +
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#scale_x_continuous(expand=c(0,0)) +
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#scale_y_continuous(expand=c(0,0)) +
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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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labs(x = NULL, y = NULL)
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}
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