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evaluate all columns in gTrack y.field when concatenating #34

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merged 3 commits into from
Mar 21, 2024
Merged

evaluate all columns in gTrack y.field when concatenating #34

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2f82def
evaluate all columns in gTrack y.field when concatenating
jrafailov Mar 14, 2024
f79465b
agnosticize aggregate to function vs x
jrafailov Mar 15, 2024
9d3ec28
agnosticize input to aggregate w/ positional arguments
jrafailov Mar 15, 2024
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38 changes: 19 additions & 19 deletions R/gTrack.R
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Original file line number Diff line number Diff line change
Expand Up @@ -404,7 +404,7 @@ setValidity('gTrack', function(object)
else T)))
problems = c(problems, 'Some nonempty trackdata edges $to and $from fields are out of bounds (ie exceed the length of the data field of the corresponding gTrack item')

if (!is.null(formatting(object)$y.field) && !is.na(formatting(object)$y.field))
if (!is.null(formatting(object)$y.field) && !all(is.na(formatting(object)$y.field)))
{
nix = !is.na(object$y.field) & sapply(dat(object), inherits, 'GRanges')
if (any(nix))
Expand Down Expand Up @@ -1959,7 +1959,7 @@ karyogram = function(file = NULL, hg19 = TRUE, bands = TRUE, arms = TRUE, tel.wi

if (arms) ## draw arms with slightly different hues of the same color and black ranges for telomere / centromere
{
tmp.tel = aggregate(formula = end ~ as.character(seqnames), data = GenomicRanges::as.data.frame(ucsc.bands), FUN = max)
tmp.tel = aggregate(end ~ as.character(seqnames), data = GenomicRanges::as.data.frame(ucsc.bands), FUN = max)
tmp.tel = structure(tmp.tel[,2], names = as.character(tmp.tel[,1]))+1
telomeres = c(GRanges(names(tmp.tel), IRanges::IRanges(start = rep(1, length(tmp.tel)), end = rep(tel.width, length(tmp.tel))),
seqlengths = GenomeInfoDb::seqlengths(seqinfo(ucsc.bands))),
Expand Down Expand Up @@ -2496,9 +2496,9 @@ draw.ranges = function(x, y = NULL, lwd = 0.5, col = "black", border = col, labe

if (nrow(x2)>0)
{
b.st = aggregate(formula = pos1 ~ group, data = x2, FUN = min)
b.en = aggregate(formula = pos2 ~ group, data = x2, FUN = max)
b.y = aggregate(formula = y ~ group, data = x2, FUN = function(x) x[1])
b.st = aggregate(pos1 ~ group, data = x2, FUN = min)
b.en = aggregate(pos2 ~ group, data = x2, FUN = max)
b.y = aggregate(y ~ group, data = x2, FUN = function(x) x[1])

seg.coord = data.frame(x0 = b.st[,2], x1 = b.en[,2], y = b.y[,2]);

Expand Down Expand Up @@ -3151,8 +3151,8 @@ draw.grl = function(grl,
{
if (is.null(y) | !is.null(ylim.subplot))
{
pos1 = aggregate(x = pos1 ~ group, data = grl.segs, FUN = min);
pos2 = aggregate(x = pos2 ~ group, data = grl.segs, FUN = max);
pos1 = aggregate(pos1 ~ group, data = grl.segs, FUN = min);
pos2 = aggregate(pos2 ~ group, data = grl.segs, FUN = max);
pos1 = structure(pos1[,2], names = pos1[,1]) - round(stack.gap/2);
pos2 = structure(pos2[,2]-1, names = pos2[,1]) + round(stack.gap/2);

Expand Down Expand Up @@ -3235,10 +3235,10 @@ draw.grl = function(grl,
}))

contig.lim = data.frame(
group = names(vaggregate(x = y.relbin ~ group, data = grl.segs, FUN = max)),
pos1 = vaggregate(x = pos1 ~ group, data = grl.segs, FUN = min) - round(stack.gap)/2,
pos2 = vaggregate(x = pos2 ~ group, data = grl.segs, FUN = max) + round(stack.gap)/2,
height = vaggregate(x = y.relbin ~ group, data = grl.segs, FUN = max)
group = names(vaggregate(y.relbin ~ group, data = grl.segs, FUN = max)),
pos1 = vaggregate(pos1 ~ group, data = grl.segs, FUN = min) - round(stack.gap)/2,
pos2 = vaggregate(pos2 ~ group, data = grl.segs, FUN = max) + round(stack.gap)/2,
height = vaggregate(y.relbin ~ group, data = grl.segs, FUN = max)
);
contig.lim$width = contig.lim$pos2 - contig.lim$pos1
contig.lim$y.bin = 0;
Expand Down Expand Up @@ -3962,10 +3962,10 @@ draw.grl = function(grl,
{
if (!draw.paths)
{
pos1 = vaggregate(x = pos1 ~ group, data = grl.segs, FUN = min);
pos2 = vaggregate(x = pos2 ~ group, data = grl.segs, FUN = max);
ywid = vaggregate(x = ywid ~ group, data = grl.segs, FUN = max);
y = vaggregate(x = y ~ group, data = grl.segs, FUN = mean);
pos1 = vaggregate(pos1 ~ group, data = grl.segs, FUN = min);
pos2 = vaggregate(pos2 ~ group, data = grl.segs, FUN = max);
ywid = vaggregate(ywid ~ group, data = grl.segs, FUN = max);
y = vaggregate(y ~ group, data = grl.segs, FUN = mean);
grl.segs.u = data.frame(group = names(pos1), pos1, pos2, y, ywid);
grl.segs.u$grl.labels = grl.props$grl.labels[match(grl.segs.u$group, grl.props$group)]
grl.segs.u$grl.cols = grl.props$grl.cols[match(grl.segs.u$group, grl.props$group)]
Expand All @@ -3984,10 +3984,10 @@ draw.grl = function(grl,
}
else
{
pos1 = vaggregate(x = pos1 ~ group, data = grl.segs, FUN = min);
pos2 = vaggregate(x = pos2 ~ group, data = grl.segs, FUN = max);
y0 = vaggregate(x = y ~ group, data = grl.segs, FUN = min);
y1 = vaggregate(x = y ~ group, data = grl.segs, FUN = max);
pos1 = vaggregate(pos1 ~ group, data = grl.segs, FUN = min);
pos2 = vaggregate(pos2 ~ group, data = grl.segs, FUN = max);
y0 = vaggregate(y ~ group, data = grl.segs, FUN = min);
y1 = vaggregate(y ~ group, data = grl.segs, FUN = max);
grl.segs.u = data.frame(group = names(pos1), pos1, pos2, y0, y1);
grl.segs.u$grl.labels = grl.props$grl.labels[match(grl.segs.u$group, grl.props$group)]
grl.segs.u$grl.cols = grl.props$grl.cols[match(grl.segs.u$group, grl.props$group)]
Expand Down
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