Tanushree Tunstall
bdbc97c40a
which annoyingly throws away lots of useful data that RShiny needs for clickable plots. Also split the "flame bar" for ligand distance out into separate functions in generate_distance_colour_map.R. This can now be easily incorporated into any "wide" graph showing all positions.
121 lines
4.6 KiB
R
121 lines
4.6 KiB
R
# takes a dataframe and returns the same dataframe with two extra columns for colours and position
|
|
generate_distance_colour_map = function(plotdf,
|
|
xvar_colname = "position",
|
|
yvar_colname = 'duet_scaled',
|
|
lig_dist_colname = "ligand_distance",
|
|
lig_dist_colours = c("green", "yellow", "orange", "red"),
|
|
#tpos0 = 0,
|
|
#tpos1 = 0,
|
|
#tpos2 = 0,
|
|
#tpos3 = 0,
|
|
debug = FALSE
|
|
)
|
|
{
|
|
#-------------------
|
|
# x and y axis
|
|
# range, scale, etc
|
|
#-------------------
|
|
my_xlim = length(unique(plotdf[[yvar_colname]])); my_xlim
|
|
ymin = min(plotdf[[yvar_colname]]); ymin
|
|
ymax = max(plotdf[[yvar_colname]]); ymax
|
|
|
|
#if (tpos0 == 0){
|
|
# tpos0 = ymin-0.5
|
|
#}
|
|
#if (tpos1 == 0){
|
|
# tpos1 = ymin-0.65
|
|
#}
|
|
#if (tpos2 == 0){
|
|
# tpos2 = ymin-0.75
|
|
#}
|
|
#if (tpos3 == 0){
|
|
# tpos3 = ymin-0.85
|
|
#}
|
|
if (debug) {
|
|
cat("\nAnnotating x-axis ~", lig_dist_colname, "requested...")
|
|
}
|
|
#-------------------------------------
|
|
# round column values: to colour by
|
|
#--------------------------------------
|
|
#plotdf = plotdf[order(plotdf[[lig_dist_colname]]),]
|
|
plotdf['lig_distR'] = round(plotdf[[lig_dist_colname]], digits = 0)
|
|
#head(plotdf['lig_distR'])
|
|
|
|
#-------------------------------------
|
|
# ligand distance range, min, max, etc
|
|
#--------------------------------------
|
|
lig_min = min(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_min
|
|
lig_max = max(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_max
|
|
lig_mean = round(mean(round(plotdf[[lig_dist_colname]]), na.rm = T)); lig_mean
|
|
|
|
#-------------------------------------
|
|
# Create mapping colour key
|
|
#--------------------------------------
|
|
# sorting removes NA, so that n_colours == length(ligD_valsR)
|
|
n_colours = length(sort(unique(round(plotdf[[lig_dist_colname]], digits = 0)))); n_colours
|
|
|
|
lig_cols = colorRampPalette(lig_dist_colours)(n_colours); lig_cols
|
|
ligD_valsR = sort(unique(round(plotdf[[lig_dist_colname]], digits = 0))); ligD_valsR
|
|
length(ligD_valsR)
|
|
|
|
if (debug) {
|
|
if (n_colours == length(ligD_valsR)) {
|
|
cat("\nStarting: mapping b/w"
|
|
, lig_dist_colname
|
|
, "and colours")
|
|
}else{
|
|
cat("\nCannot start mapping b/w", lig_dist_colname, "and colours..."
|
|
, "\nLength mismatch:"
|
|
, "No. of colours: ", n_colours
|
|
, "\nValues to map:", length(ligD_valsR))
|
|
}
|
|
}
|
|
|
|
ligDcolKey <- data.frame(ligD_colours = lig_cols
|
|
, lig_distR = ligD_valsR); ligDcolKey
|
|
names(ligDcolKey)
|
|
if (debug) {
|
|
cat("\nSuccessful: Mapping b/w", lig_dist_colname, "and colours")
|
|
}
|
|
#-------------------------------------
|
|
# merge colour key with plotdf
|
|
#--------------------------------------
|
|
plotdf = merge(plotdf, ligDcolKey, by = 'lig_distR')
|
|
|
|
plotdf_check = as.data.frame(cbind(position = plotdf[[xvar_colname]]
|
|
, ligD = plotdf[[lig_dist_colname]]
|
|
, ligDR = plotdf$lig_distR
|
|
, ligD_cols = plotdf$ligD_colours))
|
|
return(plotdf)
|
|
}
|
|
|
|
generate_distance_legend = function(plotdf,
|
|
yvar_colname,
|
|
xvar_colname = 'position',
|
|
lig_dist_colname = "ligand_distance",
|
|
legend_title = "Ligand\nDistance"
|
|
)
|
|
{
|
|
# build legend for ligand distance "heat bar"
|
|
lig_min = min(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_min
|
|
lig_max = max(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_max
|
|
lig_mean = round(mean(round(plotdf[[lig_dist_colname]]), na.rm = T)); lig_mean
|
|
|
|
labels = seq(lig_min, lig_max, len = 5); labels
|
|
labelsD = round(labels, digits = 0); labelsD
|
|
|
|
get_legend(ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
|
|
, y = yvar_colname)) +
|
|
|
|
geom_tile(aes(fill = .data[[lig_dist_colname]])
|
|
, colour = "white") +
|
|
scale_fill_gradient2(midpoint = lig_mean
|
|
, low = "green"
|
|
, mid = "yellow"
|
|
, high = "red"
|
|
, breaks = labels
|
|
, limits = c(lig_min, lig_max)
|
|
, labels = labelsD
|
|
, name = legend_title)
|
|
)
|
|
}
|