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Dev max cells #1556

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merged 2 commits into from
Aug 11, 2022
Merged

Dev max cells #1556

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c3d509b
enable user specification of maxCells parameter for bulk tracks
rcorces Aug 11, 2022
106462c
fix bug when `highlight = NULL`
rcorces Aug 11, 2022
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33 changes: 25 additions & 8 deletions R/ArchRBrowser.R
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Original file line number Diff line number Diff line change
Expand Up @@ -677,6 +677,8 @@ ArchRBrowserTrack <- function(...){
#' @param downstream The number of basepairs downstream of the transcription start site of `geneSymbol` to extend the plotting window.
#' If `region` is supplied, this argument is ignored.
#' @param tileSize The numeric width of the tile/bin in basepairs for plotting ATAC-seq signal tracks. All insertions in a single bin will be summed.
#' @param maxCells The maximum number of cells to use for obtaining data to plot as a bulk track. Using more cells can increase the resolution of your plots
#' at the expense of increased processing time.
#' @param minCells The minimum number of cells contained within a cell group to allow for this cell group to be plotted. This argument can be
#' used to exclude pseudo-bulk replicates generated from low numbers of cells.
#' @param normMethod The name of the column in `cellColData` by which normalization should be performed. The recommended and default value
Expand Down Expand Up @@ -729,7 +731,8 @@ plotBrowserTrack <- function(
log2Norm = TRUE,
upstream = 50000,
downstream = 50000,
tileSize = 250,
tileSize = 250,
maxCells = 500,
minCells = 25,
normMethod = "ReadsInTSS",
highlight = NULL,
Expand Down Expand Up @@ -763,6 +766,7 @@ plotBrowserTrack <- function(
.validInput(input = upstream, name = "upstream", valid = c("integer"))
.validInput(input = downstream, name = "downstream", valid = c("integer"))
.validInput(input = tileSize, name = "tileSize", valid = c("integer"))
.validInput(input = maxCells, name = "maxCells", valid = c("integer"))
.validInput(input = minCells, name = "minCells", valid = c("integer"))
.validInput(input = normMethod, name = "normMethod", valid = c("character"))
.validInput(input = highlight, name = "highlight", valid = c("granges", "null"))
Expand Down Expand Up @@ -832,7 +836,8 @@ plotBrowserTrack <- function(
region = region[x],
tileSize = tileSize,
groupBy = groupBy,
threads = threads,
threads = threads,
maxCells = maxCells,
minCells = minCells,
pal = pal,
ylim = ylim,
Expand Down Expand Up @@ -1005,7 +1010,8 @@ plotBrowserTrack <- function(
.bulkTracks <- function(
ArchRProj = NULL,
region = NULL,
tileSize = 100,
tileSize = 100,
maxCells = 500,
minCells = 25,
groupBy = "Clusters",
useGroups = NULL,
Expand Down Expand Up @@ -1037,6 +1043,7 @@ plotBrowserTrack <- function(
groupBy = groupBy,
normMethod = normMethod,
useGroups = useGroups,
maxCells = maxCells,
minCells = minCells,
region = region,
tileSize = tileSize,
Expand Down Expand Up @@ -1098,7 +1105,9 @@ plotBrowserTrack <- function(
.gg_guides(fill = FALSE, colour = FALSE) + ggtitle(title)

#Determine Whether To Highlight
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
if(!is.null(highlight)) {
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
}
if(length(highlight) > 0){

#Data Frame
Expand Down Expand Up @@ -1455,7 +1464,9 @@ plotBrowserTrack <- function(
}

#Determine Whether To Highlight
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
if(!is.null(highlight)) {
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
}
if(length(highlight) > 0){

#Data Frame
Expand Down Expand Up @@ -1588,7 +1599,9 @@ plotBrowserTrack <- function(
}

#Determine Whether To Highlight
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
if(!is.null(highlight)) {
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
}
if(length(highlight) > 0){

#Data Frame
Expand Down Expand Up @@ -1739,7 +1752,9 @@ plotBrowserTrack <- function(
}

#Determine Whether To Highlight
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
if(!is.null(highlight)) {
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
}
if(length(highlight) > 0){

#Data Frame
Expand Down Expand Up @@ -1922,7 +1937,9 @@ plotBrowserTrack <- function(
.gg_guides(fill = FALSE, colour = FALSE) + ggtitle(title)

#Determine Whether To Highlight
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
if(!is.null(highlight)) {
highlight <- subsetByOverlaps(highlight, region, ignore.strand=TRUE)
}
if(length(highlight) > 0){

#Data Frame
Expand Down