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auxiliary_gwastree_plotting_functions.R
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#!/usr/bin/R
# -------------------------------------------
# Auxiliary functions for plotting gwas tree:
# -------------------------------------------
library(circlize)
library(dendextend)
library(ComplexHeatmap)
library(dplyr)
library(viridis)
# ------------------------
# Tree plotting functions:
# ------------------------
# Reduced circleplot FN:
plot.labels.track = function(dend){
NLAB = length(labels(dend))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
circos.text(1:NLAB-0.5, rep(0, NLAB), labels(dend), col = labels_colors(dend), cex=.25,
facing = "clockwise", niceFacing=TRUE, adj = c(0, 0.5)) }, bg.border = NA, track.height = 0.1)
}
plot.metadata.track = function(colmat, track.height=0.075, reduced.metadata=FALSE){
if (reduced.metadata) {
colmat = as.matrix(colmat[,1])
}
ncat = ncol(colmat)
track.height = track.height / 5 * ncat
circos.track(ylim = c(0, ncat), bg.border = NA, panel.fun = function(x, y) {
m = t(colmat[,ncat:1])
nr = nrow(m)
nc = ncol(m)
for(i in 1:nr) {
circos.rect(1:nc - 1, rep(nr - i, nc),
1:nc, rep(nr - i + 1, nc),
border = NA, col = m[i, ])
} }, track.height=track.height)
}
plot.circos.tree = function(dend, ntdf=NULL, track.height=0.5, curved.lines=FALSE, boxdf=NULL, boxlabdf=NULL, boxhoriz=FALSE) {
max_height = max(attr(dend, "height"))
circos.track(ylim = c(0, max_height), panel.fun = function(x, y) {
# circos.dendrogram(dend, max_height = max_height)
circos.dendrogram.internal(dend, max_height = max_height, curved.lines=curved.lines)
if (!is.null(ntdf)){
# Separate nodes that are on the left vs. right by adj.
if (is.null(ntdf$cex)){ ntdf$cex = .35 }
ntdf$face = 0
ntdf$face[ntdf$X1 <= 209] = 1
ntdf$face[ntdf$X1 >= 626] = 1
ntdf$top = sapply(ntdf$X1, function(x){
abs(min(x %% 833, (x + 418) %% 833) - 209)/209})
ntdf$top = ntdf$top * (2 * (ntdf$X1 < 418) - 1)
# diff to max height:
ntdf$maxy = max_height - ntdf$X2 - .05 # tolerance
ntdf$maxy = sapply(ntdf$maxy, function(x){min(0.5, x)})
ntdf$ry = runif(nrow(ntdf), min=min(.05, ntdf$maxy),
max=ntdf$maxy)
# TODO: Avoid collisions by making the ones next to each other change dist.
lndf = ntdf[ntdf$face == 0,]
rndf = ntdf[ntdf$face == 1,]
if (nrow(rndf) > 0){
circos.text(rndf$X1 + ux(5 * rndf$top, "mm"), (max_height - rndf$X2) - rndf$ry, rndf$symbol,
col=rndf$color, cex=rndf$cex, facing = "downward", niceFacing=TRUE, adj = c(1, 1))
# Draw line between node and text:
circos.segments(x0=rndf$X1, y0=max_height - rndf$X2, x1=rndf$X1 + ux(5 * rndf$top, "mm"),
y1=max_height - rndf$X2 - rndf$ry + 0.01, straight=TRUE, col=rndf$color)
}
if (nrow(lndf) > 0){
circos.text(lndf$X1 + ux(-5 * lndf$top, "mm"), (max_height - lndf$X2) - lndf$ry, lndf$symbol,
col=lndf$color, cex=lndf$cex, facing = "downward", niceFacing=TRUE, adj = c(0, 1))
# Draw line between node and text:
circos.segments(x0=lndf$X1, y0=max_height - lndf$X2, x1=lndf$X1 + ux(-5 * lndf$top, "mm"),
y1=max_height - lndf$X2 - lndf$ry + 0.01, straight=TRUE, col=lndf$color)
}
}
if (!is.null(boxdf)){ add.circos.boxes(boxdf, boxlabdf, boxhoriz=boxhoriz) }
}, track.height=track.height, bg.border = NA)
}
# Auxiliary for circosplot:
plot.rna.avail = function(rna.avail, scale=1){
circos.track(ylim = c(0, 1), bg.border = NA, panel.fun = function(x, y) {
for(i in which(rna.avail == 1)) {
circos.rect(i - 1, 0, i, 1,
col='grey25', border=NA)
} }, track.height=0.0075 * scale)
}
# Auxiliary for circosplot:
plot.hit.track = function(hit.track, scale=1){
hpal = rev(magma(100))[10:100]
top.nhit = max(max(hit.track$nhit), 1)
hbins <- cut(1:top.nhit, seq(0, top.nhit, length.out=length(hpal)), include.lowest=T)
hcol = hpal[hbins]
circos.track(ylim = c(0, 1), bg.border = NA, panel.fun = function(x, y) {
for(j in 1:nrow(hit.track)) {
i = hit.track$i[j]
nhit = hit.track$nhit[j]
circos.rect(i - 1, 0, i, 1,
col=hcol[nhit], border=NA)
} }, track.height=0.005 * scale)
}
plot.leafpval.track = function(leaf.pval, cutp=CUTP, scale=1){
ind = which(leaf.pval > 0)
if (length(ind) > 0){
lp = leaf.pval[ind]
palette = col4
# Color for strength of p-value:
bins <- cut(lp, seq(0, cutp, length.out=length(palette)), include.lowest=T)
lcol = palette[bins]
circos.track(ylim = c(0, 1), bg.border = NA, panel.fun = function(x, y) {
for(j in 1:length(ind)) {
i = ind[j]
circos.rect(i - 1, 0, i, 1,
col=lcol[j], border=NA)
} }, track.height=0.005 * scale)
}
}
plot.fractional.tracks = function(udf, fractional=TRUE, fulltrack=TRUE, scale=1){
# Add barplots:
nr = nrow(udf)
udf$col = as.character(udf$col)
if (fulltrack){
topy = max(udf$total)
circos.track(ylim = c(0, topy), bg.border = NA, panel.fun = function(x, y) {
for(i in 1:nr) {
circos.rect(rep(i - 1, 2),c(0, udf$uq[i]),
rep(i, 2),c(udf$uq[i], udf$total[i]),
col=c(udf$col[i], 'grey85'), border=NA)
} }, track.height=0.06 * scale)
}
if (fractional){
circos.track(ylim = c(0, 1), bg.border = NA, panel.fun = function(x, y) {
for(i in 1:nr) {
circos.rect(rep(i - 1, 2),c(0, udf$frac[i]),
rep(i, 2),c(udf$frac[i], 1),
col=c(udf$col[i], 'grey85'), border=NA)
} }, track.height=0.06 * scale)
}
}
add.circos.boxes = function(boxdf, boxlabdf=NULL, boxhoriz=FALSE){
circos.rect(boxdf$X1, boxdf$Y1,
boxdf$X2, boxdf$Y2 - max_height * 0.005,
lwd=boxdf$lwd, lty='dashed', col=NA,border=boxdf$col)
if(!is.null(boxlabdf)){
if (boxhoriz) {
facing='downward'
fix.adj=TRUE
adj = 0.925
} else {
facing='reverse.clockwise'
adj = 0.975
fix.adj=FALSE
}
circos.segments(boxlabdf$X1, adj * max_height - boxlabdf$X2,
boxlabdf$X1, max_height - boxlabdf$X2)
par(xpd=NA)
if (fix.adj){
boxlabdf$hadj = (cos((NLAB - boxlabdf$X1)/NLAB * 2* pi) + 1 ) / 2
boxlabdf$vadj = (sin((NLAB - boxlabdf$X1)/NLAB * 2* pi) + 1 ) / 2
for (i in 1:nrow(boxlabdf)) {
circos.text(boxlabdf$X1[i], adj * max_height - boxlabdf$X2[i], as.character(boxlabdf$node)[i],
col=boxdf$col[i], cex=.75, facing=facing, niceFacing=TRUE, adj=c(boxlabdf$hadj[i], boxlabdf$vadj[i]))
}
} else {
circos.text(boxlabdf$X1, adj * max_height - boxlabdf$X2, as.character(boxlabdf$node),
col=boxdf$col, cex=.75, facing=facing, niceFacing=TRUE, adj=c(0, 0.5))
}
par(xpd=FALSE)
}
}
# Full plotting function:
circleplot = function(dend, lab, with.tree=TRUE, nodedf=NULL, udf=NULL,
# For plotting metadata:
add.metadata=TRUE, hit.track=NULL, scale=1,
reduced.metadata=FALSE, curved.lines=FALSE,
leaf.pval=NULL, rna.avail=NULL, plot.labels=TRUE,
# For plotting tracks around:
fractional=TRUE, fulltrack=TRUE, cutp=CUTP,
boxdf=NULL, boxlabdf=NULL, boxhoriz=FALSE){
# Set up dendrogram:
NLAB = length(labels(dend))
mll = meta.image(metamat[lab,5:1], colvals=colvals, cex=.6, horiz=TRUE, return.mat=TRUE)
nummat = mll[[1]]
colsmeta = mll[[2]]
colmat = matrix(colsmeta[nummat], nrow=nrow(nummat))
labels_dend <- labels(dend)
if (as.logical(anyDuplicated(labels_dend))) {
labels(dend) <- paste0(seq_along(labels_dend), "_", labels_dend)
labels_dend <- labels(dend) }
# Initialize figure:
circos.par(cell.padding = c(0, 0, 0, 0), track.margin=rep(0.001,2))
circos.initialize(factors = "single", xlim = c(0, NLAB))
# Plot tracks:
if (plot.labels){ plot.labels.track(dend) }
if (!is.null(hit.track)){ plot.hit.track(hit.track, scale=scale) }
if (!is.null(leaf.pval)){ plot.leafpval.track(leaf.pval, cutp, scale=scale) }
if (!is.null(udf)){ plot.fractional.tracks(udf, fractional=fractional, fulltrack=fulltrack, scale=1) }
if (!is.null(rna.avail)){ plot.rna.avail(rna.avail, scale=scale) }
if (add.metadata){ plot.metadata.track(colmat, track.height=0.075 * scale, reduced.metadata=reduced.metadata) }
if (with.tree){ plot.circos.tree(dend, ntdf=nodedf, track.height=0.5, curved.lines=curved.lines, boxdf=boxdf, boxlabdf=boxlabdf, boxhoriz=boxhoriz) }
circos.clear()
circos.clear()
}
# Same as above, but split:
circleplot_split = function(dend, lab, NCLUST, with.tree=TRUE, only.diff=FALSE, nodedf=NULL, curved.lines=FALSE){
# Set up dendrogram:
NLAB = length(labels(dend))
mll = meta.image(metamat[lab,5:1], colvals=colvals, cex=.6, horiz=TRUE, return.mat=TRUE)
nummat = mll[[1]]
colsmeta = mll[[2]]
colmat = matrix(colsmeta[nummat], nrow=nrow(nummat))
labels_dend <- labels(dend)
if (as.logical(anyDuplicated(labels_dend))) {
labels(dend) <- paste0(seq_along(labels_dend), "_", labels_dend)
labels_dend <- labels(dend) }
# Plot figure:
# Make split dendrogram:
colpair = colorRampPalette(brewer.pal(n=12,name="Paired"))(NCLUST)
dend <- color_branches(dend, k=NCLUST, col=colpair)
dend = set(dend, "labels_cex", .18)
labels_dend <- labels(dend)
if (as.logical(anyDuplicated(labels_dend))) {
labels(dend) <- paste0(seq_along(labels_dend), "_", labels_dend)
labels_dend <- labels(dend)
}
# Factors/splits:
kcol = unlist(get_leaves_attr(dend, 'edgePar'))
letext = c(letters, paste0('a', letters))
factors = letext[as.numeric(factor(kcol, levels = unique(kcol)))]
dend_list = get_subdendrograms(dend, k=NCLUST)
# Correct the dendrogram order:
dnames = sapply(dend_list, function(x){as.numeric(strsplit(labels(x)[1],'_')[[1]][[1]]) })
names(dend_list) = letext[1:NCLUST][order(order(dnames))]
# ----------------
# Plot dendrogram:
circos.par(cell.padding = c(0, 0, 0, 0), track.margin=rep(0.001,2))
circos.initialize(factors, xlim = cbind(c(0, 0), table(factors)))
# Text labels:
circos.track(ylim = c(0, 1),
panel.fun = function(x, y) {
sector.index = CELL_META$sector.index
dend = dend_list[[sector.index]]
txt = labels(dend)
nc = length(txt)
circos.text(1:nc-0.5, rep(0, nc), txt,
col = labels_colors(dend), cex=.25,
facing = "clockwise", niceFacing=TRUE, adj = c(0, 0.5))
}, bg.border = NA, track.height = 0.1)
# Metadata:
circos.track(ylim = c(0, 5), bg.border = NA, panel.fun = function(x, y) {
sector.index = CELL_META$sector.index
m = t(colmat[factors == sector.index,5:1])
nr = nrow(m)
nc = ncol(m)
for(i in 1:nr) {
circos.rect(1:nc - 1, rep(nr - i, nc),
1:nc, rep(nr - i + 1, nc),
border = NA, col = m[i, ])
} }, track.height=0.125)
# Dendrogram
max_height = max(sapply(dend_list, function(x) attr(x, "height")))
circos.track(ylim = c(0, max_height), bg.border = NA, track.height = 0.3,
panel.fun = function(x, y) {
sector.index = CELL_META$sector.index
dend = dend_list[[sector.index]]
# circos.dendrogram(dend, max_height = max_height)
circos.dendrogram.internal(dend, max_height = max_height, curved.lines=curved.lines)
if (!is.null(nodedf)){
circos.text(nodedf$V1, max_height - nodedf$V2, as.character(nodedf$node),
col = 'black', cex=.25,
facing = "reverse.clockwise", niceFacing=TRUE, adj = c(0, 0.5))
}
}
)
}
calculate.curve = function(x1,x2, y1,y2, curve=NULL) {
# TODO check direction:
if (is.null(curve)){
# Curve for connecting line:
sq = seq(-4,max(y1 - y2 * 20, 8), length.out=50)
curve = 1/ (1 + exp(-sq))
curve = (curve - min(curve)) / (diff(range(curve)))
}
x = (curve * (x1 - x2)) + x2
y = seq(y2, y1, length.out=length(curve))
return(list(x=x, y=y))
}
# ------------------------------------------------------------------------------
# Dendrogram plotting:
# Same as function in: https://github.com/jokergoo/circlize/blob/master/R/plot.R
# Changes: Skips plotting lty = 0 (no-line)
# ------------------------------------------------------------------------------
circos.dendrogram.internal = function(dend, facing = c("outside", "inside"),
max_height = NULL, use_x_attr = FALSE,
curved.lines=FALSE) {
facing = match.arg(facing)[1]
if(is.null(max_height)) { max_height = attr(dend, "height") }
is.leaf = function(object) {
leaf = attr(object, "leaf")
if(is.null(leaf)) { FALSE } else { leaf }
}
use_x_attr = use_x_attr
lines_par = function(col = par("col"), lty = par("lty"), lwd = par("lwd"), ...) { return(list(col = col, lty = lty, lwd = lwd)) }
points_par = function(col = par("col"), pch = par("pch"), cex = par("cex"), ...) { return(list(col = col, pch = pch, cex = cex)) }
draw.d = function(dend, max_height, facing = "outside", max_width = 0) {
leaf = attr(dend, "leaf")
d1 = dend[[1]] # child tree 1
d2 = dend[[2]] # child tree 2
height = attr(dend, "height")
midpoint = attr(dend, "midpoint")
if(use_x_attr) {
x1 = attr(d1, "x")
} else {
if(is.leaf(d1)) {
x1 = x[as.character(attr(d1, "label"))]
} else {
x1 = attr(d1, "midpoint") + x[as.character(labels(d1))[1]]
}
}
y1 = attr(d1, "height")
if(use_x_attr) {
x2 = attr(d2, "x")
} else {
if(is.leaf(d2)) {
x2 = x[as.character(attr(d2, "label"))]
} else {
x2 = attr(d2, "midpoint") + x[as.character(labels(d2))[1]]
}
}
y2 = attr(d2, "height")
# graphic parameter for current branch
# only for lines, there are lwd, col, lty
edge_par1 = do.call("lines_par", as.list(attr(d1, "edgePar"))) # as.list to convert NULL to list()
edge_par2 = do.call("lines_par", as.list(attr(d2, "edgePar")))
node_par = attr(dend, "nodePar")
if(!is.null(node_par)) node_par = do.call("points_par", as.list(attr(dend, "nodePar")))
if (curved.lines){
if(facing == "outside") {
if (edge_par1$lty != 0){
lxy = calculate.curve(x1=x1, x2=(x1 + x2)/2, y1=max_height - y1,
y2=max_height - height, curve=NULL)
circos.lines(lxy$x, lxy$y, col=edge_par1$col, lty=edge_par1$lty,
lwd=edge_par1$lwd, straight=TRUE)
# lwd=0.1, straight=TRUE)
}
if (edge_par2$lty != 0){
lxy = calculate.curve(x1=x2, x2=(x1 + x2)/2, y1=max_height - y2,
y2=max_height - height, curve=NULL)
circos.lines(lxy$x, lxy$y, col=edge_par2$col, lty=edge_par2$lty,
lwd=edge_par2$lwd, straight=TRUE)
# lwd=0.1, straight=TRUE)
}
if(!is.null(node_par)) {
circos.points((x1+x2)/2, max_height - height, col = node_par$col,
pch = node_par$pch, cex = node_par$cex)
}
} else if(facing == "inside") {
if (edge_par1$lty != 0){
lxy = calculate.curve(x1=x1, x2=(x1 + x2)/2,
y1=y1, y2=height, curve=NULL)
circos.lines(lxy$x, lxy$y, col=edge_par1$col, lty=edge_par1$lty,
lwd=edge_par1$lwd, straight=TRUE)
}
if (edge_par2$lty != 0){
lxy = calculate.curve(x1=x2, x2=(x1 + x2)/2,
y1=y2, y2=height, curve=NULL)
circos.lines(lxy$x, lxy$y, col=edge_par2$col, lty=edge_par2$lty,
lwd=edge_par2$lwd, straight=TRUE)
}
if(!is.null(node_par)) {
circos.points((x1+x2)/2, height, col = node_par$col,
pch = node_par$pch, cex = node_par$cex)
}
}
} else {
if(facing == "outside") {
if (edge_par1$lty != 0){
circos.lines(c(x1, x1), max_height - c(y1, height), col=edge_par1$col,
lty=edge_par1$lty, lwd=edge_par1$lwd, straight=TRUE)
circos.lines(c(x1, (x1+x2)/2), max_height - c(height, height), col=edge_par1$col,
lty=edge_par1$lty, lwd=edge_par1$lwd)
}
if (edge_par2$lty != 0){
circos.lines(c(x2, x2), max_height - c(y2, height), col=edge_par2$col,
lty=edge_par2$lty, lwd=edge_par2$lwd, straight=TRUE)
circos.lines(c(x2, (x1+x2)/2), max_height - c(height, height), col=edge_par2$col,
lty=edge_par2$lty, lwd=edge_par2$lwd)
}
if(!is.null(node_par)) {
circos.points((x1+x2)/2, max_height - height, col = node_par$col,
pch = node_par$pch, cex = node_par$cex)
}
} else if(facing == "inside") {
if (edge_par1$lty != 0){
circos.lines(c(x1, x1), c(y1, height), col = edge_par1$col,
lty = edge_par1$lty, lwd = edge_par1$lwd, straight = TRUE)
circos.lines(c(x1, (x1+x2)/2), c(height, height), col = edge_par1$col,
lty = edge_par1$lty, lwd = edge_par1$lwd)
}
if (edge_par2$lty != 0){
circos.lines(c(x2, x2), c(y2, height), col = edge_par2$col,
lty = edge_par2$lty, lwd = edge_par2$lwd, straight = TRUE)
circos.lines(c(x2, (x1+x2)/2), c(height, height), col = edge_par2$col,
lty = edge_par2$lty, lwd = edge_par2$lwd)
}
if(!is.null(node_par)) {
circos.points((x1+x2)/2, height, col = node_par$col,
pch = node_par$pch, cex = node_par$cex)
}
}
}
# do it recursively
if(is.leaf(d1)) {
node_par = attr(d1, "nodePar")
if(!is.null(node_par)) node_par = do.call("points_par", as.list(attr(d1, "nodePar")))
if(facing == "outside") {
if(!is.null(node_par)) {
circos.points(x1, max_height, col = node_par$col, pch = node_par$pch, cex = node_par$cex)
}
} else if(facing == "inside") {
if(!is.null(node_par)) {
circos.points(x1, 0, col = node_par$col, pch = node_par$pch, cex = node_par$cex)
}
}
} else {
draw.d(d1, max_height, facing, max_width)
}
if(is.leaf(d2)) {
node_par = attr(d2, "nodePar")
if(!is.null(node_par)) node_par = do.call("points_par", as.list(attr(d2, "nodePar")))
if(facing == "outside") {
if(!is.null(node_par)) {
circos.points(x2, max_height, col = node_par$col, pch = node_par$pch, cex = node_par$cex)
}
} else if(facing == "inside") {
if(!is.null(node_par)) {
circos.points(x2, 0, col = node_par$col, pch = node_par$pch, cex = node_par$cex)
}
}
} else {
draw.d(d2, max_height, facing, max_width)
}
}
labels = as.character(labels(dend))
x = seq_along(labels) - 0.5
names(x) = labels
n = length(labels)
draw.d(dend, max_height, facing, max_width = n)
}