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added wideplot subcols generation within bp_subcolours.R to make it easier to call the whole thing as a function and use merged_df3 to generate plot without having to separately generate special data for it. Tested with real data on different stability params

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Tanushree Tunstall 2021-09-15 19:29:09 +01:00
parent 449af7acf4
commit 7550efbd4c
2 changed files with 80 additions and 3 deletions
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81
scripts/functions/bp_subcolours.R
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@ -3,7 +3,7 @@
# LINK: https://stackoverflow.com/questions/49818271/stacked-barplot-with-colour-gradients-for-each-bar
#########################################################
ColourPalleteMulti <- function(df, group, subgroup){
ColourPalleteMulti = function(df, group, subgroup){
# Find how many colour categories to create and the number of colours in each
categories <- aggregate(as.formula(paste(subgroup, group, sep="~" ))
@ -24,4 +24,81 @@ ColourPalleteMulti <- function(df, group, subgroup){
, category.end[i]))(categories[i,2])}))
return(colours)
}
#########################################################
#########################################################################
bp_stability_hmap <- function(plotdf = merged_df3
, xvar_colname = "position"
#, bar_col_colname = "group"
, stability_colname = "duet_scaled"
, stability_outcome_colname = "duet_outcome"
, p_title = "" # "Protein stability (DUET)"
, my_xaxls = 12 # x-axis label size
, my_yaxls = 20 # y-axis label size
, my_xaxts = 18 # x-axis text size
, my_yaxts = 20 # y-axis text size
, my_pts = 20 # plot-title size
, my_xlab = "Position"
, my_ylab = "No. of nsSNPs"
)
{
# order the df by position and ensure it is a factor
plotdf = plotdf[order(plotdf[[xvar_colname]]), ]
plotdf[[xvar_colname]] = factor(plotdf[[xvar_colname]])
#cat("\nSneak peak:\n")
head(data.frame( plotdf[[xvar_colname]], plotdf[[stability_colname]] ) )
# stability values isolated to help with generating column called: 'group'
my_grp = plotdf[[stability_colname]]
cat( "\nLength of nsSNPs:", length(my_grp)
, "\nLength of unique values for nsSNPs:", length(unique(my_grp)) )
# Add col: 'group'
plotdf$group = paste0(plotdf[[stability_outcome_colname]], "_", my_grp, sep = "")
# check unique values in normalised data
cat("\nNo. of unique values in", stability_colname, "no rounding:"
, length(unique(plotdf[[stability_colname]])))
# Call the function to create the palette based on the group defined above
#subcols_ps
subcols_bp_hmap = ColourPalleteMulti(plotdf, stability_outcome_colname, stability_colname)
cat("\nNo. of sub colours generated:", length(subcols_bp_hmap))
#-------------------------------
# Generate the subcols barplot
#-------------------------------
#g = ggplot(plotdf, aes(x = factor(position, ordered = T)))
g = ggplot(plotdf, aes_string(x = xvar_colname
# , ordered = T)
))
OutWidePlot = g + geom_bar(aes(fill = group)
, colour = "grey") +
scale_fill_manual( values = subcols_bp_hmap
, guide = "none") +
theme( axis.text.x = element_text(size = my_xaxls
, angle = 90
, hjust = 1
, vjust = 0.4)
, axis.text.y = element_text(size = my_yaxls
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = my_xaxts)
, 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)
return(OutWidePlot)
}