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Fixes Different Json creation when using annotations #129

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Fixes Different Json creation when using annotations #129

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f212276
Fixes Different Json creation when using annotations
Jan 16, 2024
d2a4819
Fixes walks json by adding unique identifiers for each node of a walk
Jan 22, 2024
254105e
Merge pull request #1 from mskilab-org/master
stanleyrc Jan 24, 2024
562f56c
Speeds up creation of arrow files by not printing every single bin
Jan 30, 2024
5453a5e
Fixes get(cid.field) error when the genome graph only has loose ends …
Jan 31, 2024
039559a
Coerces col (for the ggraph json function), which is used in gtrack t…
Feb 13, 2024
62531fd
make genome json work with objects without edges and weights
Mar 8, 2024
200ec44
adds ability for offset for allelic genome graphs. temporary fix. In …
Mar 11, 2024
93f01b6
updates
Apr 16, 2024
879ac70
Merge branch 'mskilab-org:master' into master
stanleyrc Jun 13, 2024
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125 changes: 88 additions & 37 deletions R/gGnome.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5801,7 +5801,8 @@ gGraph = R6::R6Class("gGraph",
settings = list(y_axis = list(title = "copy number",
visible = TRUE)),
cid.field = NULL,
no.y = FALSE)
no.y = FALSE,
offset = FALSE)
{
## Make sure that our nodes are not empty before visualizing
if (is.null(private$pnodes) || length(private$pnodes) == 0) {
Expand Down Expand Up @@ -5838,23 +5839,24 @@ gGraph = R6::R6Class("gGraph",

if (length(nfields))
{
nfields = setdiff(intersect(nfields, names(self$nodes$dt)), names(node.json))
node.json = cbind(node.json, gr2dt(self$nodes$gr)[, nfields, with = FALSE])
nfields = setdiff(intersect(nfields, names(self$nodes$dt)), names(node.json))
node.json = cbind(node.json, gr2dt(self$nodes$gr)[, nfields, with = FALSE])

}
.dtstring = function(dt)
dt[, gsub('\\|+', '|', gsub('\\|+$', '', gsub('^\\|+', '', do.call(paste, c(lapply(names(.SD), function(x) ifelse(!is.na(.SD[[x]]), paste0(x, '=', .SD[[x]]), '')), sep = '|')))))]

if (!is.null(annotations))
{
nodes.overlap.annotations = intersect(annotations, names(values(self$nodes$gr)))
if (length(nodes.overlap.annotations) == 0){
if (length(nodes.overlap.annotations) == 0) {
warning('There is no overlap between the provided annotations and the annotaions available in the nodes in your gGraph.')
node.json$annotation = ''
} else {
node.json = cbind(node.json, data.table(annotation = .dtstring(as.data.table(values(self$nodes$gr))[, intersect(annotations, names(values(self$nodes$gr))), with = FALSE])))
}
}

if (is.null(cid.field)){
cid.field = 'sedge.id'
} else {
Expand Down Expand Up @@ -5888,11 +5890,11 @@ gGraph = R6::R6Class("gGraph",
ed$annotation = .dtstring(ed[, intersect(names(ed), annotations), with = FALSE])
}
ed$from = private$pnodes$snode.id[ed$from]
ed$to = -private$pnodes$snode.id[ed$to]
ed$to = private$pnodes$snode.id[ed$to]
}
}

yf = NULL

if (!no.y && !is.null(yf <- self$meta$y.field) && yf %in% names(values(self$nodes$gr)))
{
settings$y.axis = yf
Expand All @@ -5901,12 +5903,10 @@ gGraph = R6::R6Class("gGraph",

if (yf %in% names(private$pedges))
ed$weight = private$pedges[.(ed$sedge.id), yf, with = FALSE]
}
else
{
} else {
no.y = TRUE
}

## make loose end nodes
if (length(self$loose)>0)
{
Expand Down Expand Up @@ -5934,11 +5934,16 @@ gGraph = R6::R6Class("gGraph",
)[, type := 'LOOSE']

## remove zero or NA weight loose ends
loose.ed = loose.ed[!is.na(weight), ][weight>0, ]
if("weight" %in% names(loose.ed)) { #fix for ggraphs to be plotted as intervals
loose.ed = loose.ed[!is.na(weight), ][weight>0, ]
}

## add cid values for loose ends
max.cid = max(ed[, get(cid.field)], na.rm = T)
loose.ed[, (cid.field) := 1:.N + max.cid]
loose.ed[, class := '']
if(nrow(ed) > 0) { #added this fix for genomes with only loose ends
max.cid = max(ed[, get(cid.field)], na.rm = T)
loose.ed[, (cid.field) := 1:.N + max.cid]
loose.ed[, class := '']
}

if (!is.null(annotations))
loose.ed$annotation = ''
Expand All @@ -5957,23 +5962,29 @@ gGraph = R6::R6Class("gGraph",
# KSK: temporary fix for old-style notation (large values instead of negatives)
# of whether edge is going out/coming in from left or right side of node
# so that json is rendered correctly in gGnome.js:
# max.node.id <- max(self$dt$node.id)
# ed[from > max.node.id, from := (from - max.node.id)*-1]
# ed[to <= max.node.id, to := -1*to]
# ed[to > max.node.id, to := (to - max.node.id)]
max.node.id <- max(self$dt$node.id)
ed[from > max.node.id, from := (from - max.node.id)*-1]
ed[to <= max.node.id, to := -1*to]
ed[to > max.node.id, to := (to - max.node.id)]
# KSK end

## TODO: do not assume things are paired up
## do not assume the cn field in the segs is correct
node.json$title = as.character(node.json$iid)
node.json[, type := "interval"]
node.json[, strand := "*"]

## if any edge left, process
if (nrow(ed)>0){
## EDGE.JSON
ed[is.na(weight), weight := 0]

## EDGE.JSON
if("weight" %in% names(loose.ed)) { #fix for ggraphs to be plotted as intervals
ed[is.na(weight), weight := 0]
} else {
ed$weight = 0
}
if(!(cid.field %in% names(ed))) {
ed[,cid.field] = ed$from #sc - added this fix for genome with no edges other than loose ends
}

ed.json = ed[,
.(cid = get(cid.field),
source = from,
Expand Down Expand Up @@ -6008,7 +6019,13 @@ gGraph = R6::R6Class("gGraph",
weight = numeric(0))
}

## append list of node metadata features if nfields is specified
## append list of node metadata features if nfields is specified
#convert name from col (used in gtrack) to color for the nodes
if("col" %in% names(node.json)) {
node.json[, color := col]
node.json[, col := NULL]
nfields = gsub("\\bcol\\b", "color",nfields) #replace only entries that start and end with col
}
if (length(nfields))
{
.fix = function(x) as.list(x)[!is.na(unlist(x))]
Expand All @@ -6035,6 +6052,22 @@ gGraph = R6::R6Class("gGraph",
if (!is.null(settings)){
gg.js = c(list(settings = settings), gg.js)
}
## tempory offset addition for allelic graphs - will probably want to be smart and only add it when major and minor overlap
if(offset) {
for(x in 1:length(gg.js$intervals)) {
col1 = gg.js$intervals[[x]]$metadata$color
if(gg.js$intervals[[x]]$y != 0) {
if(col1 == "#0000FF80") {
gg.js$intervals[[x]]$y = gg.js$intervals[[x]]$y + 0.1
} else if(col1 == "#FF000080") {
gg.js$intervals[[x]]$y = gg.js$intervals[[x]]$y - 0.1
}
}
}
}
gg.js$connections = gg.js$connections[weight != 0,]



if (save){
if (verbose)
Expand Down Expand Up @@ -7880,17 +7913,32 @@ gWalk = R6::R6Class("gWalk", ## GWALKS
warning(sprintf('Invalid efields value/s provided: "%s". These fields were not found in the gWalk and since will be ignored.', paste(missing_efields, collapse = '" ,"')))
efields = intersect(efields, names(self$edges$dt))
}

############ temporary fix for json unique iids/cids - SC start
sedu = dunlist(self$sedge.id)
cids = lapply(unname(split(cbind(data.table(cid = sedu$V1,
source = self$graph$edges[sedu$V1]$left$dt$snode.id,
sink = -self$graph$edges[sedu$V1]$right$dt$snode.id, # notice that we need to add negative sign here to meet the gGnome.js expectations
title = "",
weight = 1),
self$graph$edges[sedu$V1]$dt[, ..efields]
), sedu$listid)),
sedu[,cid := 1:.N, by = "listid"]
sedu[,source := self$graph$edges[sedu$V1]$left$dt$snode.id]
sedu[,sink := -self$graph$edges[sedu$V1]$right$dt$snode.id]
sedu[,source2 := ifelse(source < 0, -cid, cid)]
## sedu[,sink2 := ifelse(sink < 0, -cid, cid)]
sedu[,sink2 := ifelse(sink < 0, (-cid - 1), (cid + 1))]
## old method of creating cids
## cids = lapply(unname(split(cbind(data.table(cid = sedu$V1,
## source = self$graph$edges[sedu$V1]$left$dt$snode.id,
## sink = -self$graph$edges[sedu$V1]$right$dt$snode.id, # notice that we need to add negative sign here to meet the gGnome.js expectations
## title = "",
## weight = 1),
## self$graph$edges[sedu$V1]$dt[, ..efields]
## ), sedu$listid)),
## function(x) unname(split(x, 1:nrow(x))))
cids = lapply(unname(split(cbind(data.table(cid = sedu$cid,
source = sedu$source2,
sink = sedu$sink2, # notice that we need to add negative sign here to meet the gGnome.js expectations
title = "",
weight = 1),
self$graph$edges[sedu$V1]$dt[, ..efields]
), sedu$listid)),
function(x) unname(split(x, 1:nrow(x))))

############ temporary fix for json unique iids/cids - SC end
snu = dunlist(self$snode.id)
snu$ys = gGnome:::draw.paths.y(self$grl) %>% unlist

Expand All @@ -7906,24 +7954,27 @@ gWalk = R6::R6Class("gWalk", ## GWALKS
warning(sprintf('Invalid nfields value/s provided: "%s". These fields were not found in the gWalk and since will be ignored.', paste(missing_nfields, collapse = '" ,"')))
nfields = intersect(nfields, names(self$edges$dt))
}
#########temporary fix for json unique iids - SC start
snu[,iid := 1:.N, by = "listid"]
#############SC end
## iids = lapply(unname(split(cbind(
## data.table(iid = abs(snu$V1)),
iids = lapply(unname(split(cbind(
data.table(iid = abs(snu$V1)),
data.table(iid = abs(snu$iid)), #modified this to iid - SC
self$graph$nodes[snu$V1]$dt[,
.(chromosome = seqnames,
startPoint = start,
endPoint = end,
y = snu$ys,
type = "interval",
strand = ifelse(snu$V1 > 0, "+", "-"),
title = abs(snu$V1))],
title = abs(snu$iid))],#title = abs(snu$V1))],
self$graph$nodes[snu$V1]$dt[,..nfields]), snu$listid)),
function(x) unname(split(x, 1:nrow(x))))

walks.js = lapply(1:length(self), function(x)
c(as.list(pids[[x]]),
list(cids = rbindlist(cids[[x]])),
list(iids = rbindlist(iids[[x]]))))

if (include.graph){
out = c(graph.js, list(walks = walks.js))
} else {
Expand Down
3 changes: 2 additions & 1 deletion R/jsUtils.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1112,7 +1112,8 @@ get_pgv_data_dir = function(outdir, patient.id = NA){
cov2cov.js = function(cov, meta.js = NULL, js.type = 'gGnome.js', field = 'ratio',
bin.width = NA, ref = NULL, cov.color.field = NULL,
convert.to.cn = TRUE, ncn.gr = NA, gg = NA){
message(paste0("reading in file: ", cov))
message(paste0("reading in file"))
#message(paste0("reading in file: ", cov))
x = readCov(cov)
overlap.seqnames = seqlevels(x)

Expand Down
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