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various heat-bar/position tile faff

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This commit is contained in:
Tanushree Tunstall 2022-08-09 18:15:54 +01:00
parent 94454d6fba
commit 5cbaef3d36
4 changed files with 140 additions and 48 deletions
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12
scripts/functions/bp_subcolours.R
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@ -2,7 +2,7 @@
# 1b: Define function: coloured barplot by subgroup
# LINK: https://stackoverflow.com/questions/49818271/stacked-barplot-with-colour-gradients-for-each-bar
#########################################################
source("~/git/LSHTM_analysis/scripts/functions/generate_distance_colour_map.R")
#source("~/git/LSHTM_analysis/scripts/functions/generate_distance_colour_map.R")
ColourPalleteMulti = function(df, group, subgroup){
@ -121,16 +121,16 @@ bp_stability_hmap <- function(plotdf = merged_df3
, axis.title.y = element_text(size = my_yaxts )
, plot.title = element_text(size = my_pts
, hjust = 0.5)) +
labs(title = p_title
, x = my_xlab
, y = my_ylab),
geom_tile(aes(, tpos0 # heat-mapped distance tiles along the bot
, width = tW0
, height = tH0)
, fill = plotdf$ligD_colours
, colour = plotdf$ligD_colours
, linetype = "blank") +
labs(title = p_title
, x = my_xlab
, y = my_ylab),
, linetype = "blank"), #end of distance-heat-bar
generate_distance_legend(plotdf),
ncol = 2,
#align = "hv",

90
scripts/functions/logoP_or.R
View file

@ -69,17 +69,17 @@ LogoPlotCustomH <- function(plot_df
# Data processing for logo plot
#################################
plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
unique_colour_map = unique(plot_df[,c("position","ligD_colours")])
unique_colour_map = unique_colour_map[order(unique_colour_map$position), ]
rownames(unique_colour_map) = unique_colour_map$position
unique_colour_map2 = unique_colour_map
unique_colour_map2$position=as.factor(unique_colour_map2$position)
unique_colour_map2$ligD_colours = as.factor(unique_colour_map2$ligD_colours)
if (rm_empty_y){
plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
cat("\nRemoving empty positions...\n")
@ -171,20 +171,18 @@ LogoPlotCustomH <- function(plot_df
, seq_type = "aa") +
#ylab("my custom height") +
theme( axis.ticks.x = element_blank()
, axis.ticks.length = unit(0, "pt")
, axis.title.x = element_blank()
, axis.text.x = element_blank() # turn this off and the below on if you want to visually
# , axis.text.x = element_blank() # turn this off and the below on if you want to visually
# verify positions.
# , axis.text.x = element_text(size = x_ats
# , angle = x_tangle
# , hjust = 1
# , vjust = 0.4
# , colour = xfont_bgc
# , margin = margin(b=0)
# )
, axis.text.x = element_text(size = x_ats
, angle = x_tangle
, colour = xfont_bgc
, vjust = 0.4
, margin = margin(t=-8,r=0,b=0,l=0, unit="mm")
)
, axis.text.y = element_text(size = y_ats
, angle = y_tangle
, hjust = 1
, vjust = 0
, colour = yfont_bgc)
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
@ -195,10 +193,11 @@ LogoPlotCustomH <- function(plot_df
, legend.position = leg_pos
, legend.direction = leg_dir
, plot.background = element_rect(fill = theme_bgc)
#, plot.background = element_blank()
, plot.margin = margin(b=0)
, panel.grid=element_blank()
, panel.background = element_rect(fill = theme_bgc)
, plot.background = element_rect(fill = theme_bgc, colour=NA)
, panel.background = element_rect(fill = "transparent", colour=NA)
)+
@ -217,36 +216,43 @@ LogoPlotCustomH <- function(plot_df
, fill = position
, colour = position
, linetype = "blank"
)
)
) +
geom_tile() +
theme(axis.text.x = element_text(size = x_ats
, angle = x_tangle
, hjust = 1
, vjust = 0.4
, colour = xfont_bgc)
, axis.text.y = element_blank()
, axis.ticks.y = element_blank()
, axis.title.x = element_text(size = x_tts
, colour = xtt_col)
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
, legend.title = element_text(size = leg_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
, legend.position = leg_pos
, legend.direction = leg_dir
, plot.background = element_rect(fill = theme_bgc)
, plot.margin = margin(t=0)
, panel.grid=element_blank()
, panel.background = element_rect(fill = theme_bgc)
theme(
axis.text.x = element_blank()
# axis.text.x = element_text(size = x_ats
# , angle = x_tangle
# , hjust = 1
# , vjust = 0.4
# , colour = xfont_bgc)
, axis.text.y = element_blank()
, axis.ticks.y = element_blank()
, axis.ticks.x = element_blank()
, axis.title.x = element_blank()
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
, legend.title = element_text(size = leg_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
, legend.position = leg_pos
, legend.direction = leg_dir
#, plot.background = element_blank()
, plot.margin = margin(t=0,b=0)
, panel.grid=element_blank()
, plot.background = element_rect(fill = theme_bgc, colour=NA)
, panel.background = element_rect(fill = "transparent", colour=NA)
#, panel.background = element_rect(fill = theme_bgc)
#, panel.background = element_blank()
) +
scale_x_discrete(x_lab, labels=factor(unique_colour_map$position)) +
#scale_x_discrete(x_lab, labels=factor(unique_colour_map$position)) +
scale_color_manual(values=unique_colour_map$ligD_colours) +
scale_fill_manual(values=unique_colour_map$ligD_colours) +
labs(y = NULL),
ncol=1, align='v', rel_heights = c(8/10,1/10)
labs(y = NULL), NULL,
position_annotation(plot_df, bg=theme_bgc),
ncol=1, align='v', rel_heights = c(16,1,-0.1, 1)
)
}
#LogoPlotCustomH(merged_df3)
}
#LogoPlotCustomH(small_df3)