R/track_interface.R
In skummerf/GenomicWidgets: interactive visualization of genomics data
#' set_track_parameters
#'
#' Setup parameters for plotting coverage signals along genome tracks.
#' Result from this function can be passed to \code{\link{plot_tracks}}
#'
#' @param object vector of bam or bigwig file names
#' @param annotation TxDb or OrganismDb object
#' @param ... additional arguments
#' @param track_names names to associate with each file
#' @param groups vector of group assignments. traces will be grouped onto
#' subplots based on group assignments (if only showing 1 region)
#' @param share_y share the y axis?
#' @param fill fillmode for line plot
#' @param showlegend show the legend?
#' @param colors colors for each bam file
#' @param mode mode for plot
#' @param annotation_position plot annotations on bottom or on top of signal
#' traces
#' @param annotation_size relative size of annotation plot
#' @param summary Summary parameters from \code{\link{set_summary_parameters}}
#' @param layout list of additional plotly layout arguments
#' @export
#' @rdname set_track_parameters
#' @name set_track_parameters
#' @aliases set_track_parameters,character-method
#'
#' @author Alicia Schep and Justin Finkle
#' @return object storing track parameters, for use in \code{\link{plot_tracks}}
#' @examples
#'
#' library(GenomicRanges)
#' library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#'
#' ## First we'll read in some sample data
#' genomation_dir <- system.file("extdata", package = "genomationData")
#' samp.file <- file.path(genomation_dir,'SamplesInfo.txt')
#' samp.info <- read.table(samp.file, header=TRUE, sep="\t",
#' stringsAsFactors = FALSE)
#' samp.info$fileName <- file.path(genomation_dir, samp.info$fileName)
#' ctcf.peaks = genomation::readBroadPeak(system.file("extdata",
#' "wgEncodeBroadHistoneH1hescCtcfStdPk.broadPeak.gz",
#' package = "genomationData"))
#' ctcf.peaks = ctcf.peaks[seqnames(ctcf.peaks) == "chr21"]
#'
#' ## resize peaks to size 1000
#' ctcf.peaks = resize(ctcf.peaks, width = 10000, fix = "center")
#'
#' ## Make track plotter
#'
#' track_params <- set_track_parameters(samp.info$fileName[1:3],
#' annotation = TxDb.Hsapiens.UCSC.hg19.knownGene,
#' track_names = samp.info$sampleName[1:3] ,
#' share_y = TRUE)
#'
#' if (interactive()){
#' plot_tracks(ctcf.peaks[1], track_params)
#' plot(ctcf.peaks[1:3], track_params)
#' }
#'
setMethod("set_track_parameters", c("character"),
function(object,
annotation = NULL,
track_names = if (!is.null(names(object)))
names(object)
else basename(object),
groups = track_names,
share_y = TRUE,
showlegend = TRUE,
colors = NULL,
fill = c("tozeroy","none"),
mode = "lines",
annotation_position = c("bottom","top"),
annotation_size = 0.25,
summary = NULL,
layout = list()){
params <- list(Class = "TrackParameters",
data = object,
annotation = unpack_transcripts(annotation),
track_names = track_names,
groups = as.factor(groups),
summary = summary,
showlegend = showlegend,
share_y = share_y,
colors = select_colors(colors,length(object)),
fill = match.arg(fill),
annotation_position = match.arg(annotation_position),
mode = mode,
annotation_size = annotation_size,
layout = layout)
do.call(new, params)
})
#' set_summary_parameters
#'
#' Setup parameters for plotting summaries along genome tracks.
#' Result from this function can be passed to \code{\link{set_track_parameters}}
#'
#' @param object SummarizedExperiment
#' @param assay_name name of assay to use
#' @param ... additional arguments
#' @param groups either vector of group assignments of name of column in object
#' colData that corresponds to vector of group assignments
#' @param showlegend show the legend?
#' @param colors colors to use
#' @param boxpoints plot individual points?
#' @param pointpos relative position of points to boxes
#' @param ytitle name for yaxis
#' @param ranges ranges corresponding to rows of object
#' @param width relative width of summary plots when plotting tracks
#' @export
#' @return object storing summary parameters, for use in
#' \code{\link{set_track_parameters}}
#' @author Alicia Schep and Justin Finkle
#' @rdname set_summary_parameters
#' @name set_summary_parameters
#' @aliases set_summary_parameters,SummarizedExperiment-method
#' set_summary_parameters,RangedSummarizedExperiment-method
#' @examples
#'
#'
#' library(GenomicRanges)
#' library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#'
#' ## we'll read in some RNA counts
#' data(rpkm_chr21)
#'
#' ## From the ranges of the rpkm object, we'll pull out the tss
#' chr21_promoters <- promoters(SummarizedExperiment::rowRanges(rpkm_chr21),
#' up = 1000, down = 1000)
#'
#' ## set summary parameters
#'
#' summary_params <- set_summary_parameters(rpkm_chr21,
#' groups = "GROUP", ranges = chr21_promoters)
#'
#' ## We'll also read in some track data to plot
#' genomation_dir <- system.file("extdata", package = "genomationData")
#' samp.file <- file.path(genomation_dir,'SamplesInfo.txt')
#' samp.info <- read.table(samp.file, header=TRUE, sep="\t",
#' stringsAsFactors = FALSE)
#' samp.info$fileName <- file.path(genomation_dir, samp.info$fileName)
#'
#' ## Make track plotter using summary parametrs
#'
#' track_params <- set_track_parameters(samp.info$fileName[1:3],
#' annotation = TxDb.Hsapiens.UCSC.hg19.knownGene,
#' track_names = samp.info$sampleName[1:3],
#' share_y = TRUE,
#' summary = summary_params)
#'
#' if (interactive()){
#' plot_tracks(rownames(rpkm_chr21)[1:3], track_params)
#' plot(chr21_promoters[1:3], track_params)
#' }
#'
setMethod("set_summary_parameters", c("SummarizedExperiment"),
function(object,
ranges,
assay_name = assayNames(object)[1],
groups = colnames(object),
colors = "blue",
showlegend = length(colors) > 1,
boxpoints = c("all","Outliers","false"),
pointpos = 0,
ytitle = "Expression",
width = 0.3){
# Check groups
if (is.null(groups)){
groups <- ""
} else if (length(groups) == 1){
if (groups %in% colnames(colData(object)))
groups <- colData(object)[,groups]
} else{
stopifnot(length(groups) == ncol(object))
}
params <- list(Class = "SummaryParameters",
data = object,
assay_name = assay_name,
groups = groups,
colors = colors,
showlegend = showlegend,
boxpoints = match.arg(boxpoints),
pointpos = pointpos,
ytitle = ytitle,
width = width,
ranges = ranges
)
do.call(new, params)
})
#' @export
#' @rdname set_summary_parameters
setMethod("set_summary_parameters", c("RangedSummarizedExperiment"),
function(object,
ranges = rowRanges(object),
assay_name = assayNames(object)[1],
groups = NULL,
colors = "blue",
showlegend = length(colors) > 1,
boxpoints = c("all","Outliers","false"),
pointpos = 0,
ytitle = "Expression",
width = 0.3){
# Check groups
if (is.null(groups)){
groups <- ""
} else if (length(groups) == 1){
if (groups %in% colnames(colData(object)))
groups <- colData(object)[,groups]
} else{
stopifnot(length(groups) == ncol(object))
}
params <- list(Class = "SummaryParameters",
data = object,
assay_name = assay_name,
groups = groups,
colors = colors,
showlegend = showlegend,
boxpoints = match.arg(boxpoints),
pointpos = pointpos,
ytitle = ytitle,
width = width,
ranges = ranges
)
do.call(new, params)
})
#' @export
#' @rdname plot_tracks
setMethod("plot_tracks", c("GenomicRanges"),
function(windows,
params,
locus_names = mcols(windows)$name,
offset = width(windows[1]) %/% 2,
xtitle =
if (length(windows) > 1) "Relative Position"
else seqnames(windows),
...,
summary_args = list()){
arglist <- modify_param_args(params, xtitle, offset, locus_names,
...)
tracks <- do.call(multi_locus_view,
c(list(windows = windows), arglist))
out <- new("GenomeTrackWidget",
tracks = tracks,
summary_width = 0,
layout = arglist$layout)
if (!is.null(params@summary)){
ix <- match(windows, params@summary@ranges)
if (any(is.na(ix))){
warning("Windows don't match ranges stored in TrackParameters ",
"for summary. Not plotting summaries.")
} else{
summary_arglist <- modify_summary_args(params,summary_args)
summary_arglist[["row_names"]] <-
rownames(params@summary@data)[ix]
summaries <- do.call(make_locus_summaries, summary_arglist)
out <- new("GenomeTrackWidget",
tracks = tracks,
summaries = summaries,
summary_width = params@summary@width,
layout = arglist$layout)
}
} else{
out <- new("GenomeTrackWidget",
tracks = tracks,
summary_width = 0,
layout = arglist$layout)
}
out
})
#' plot_tracks
#'
#' @param windows GenomicRanges or rownames for summary object
#' @param params TrackParameters, from \code{\link{set_track_parameters}}
#' @param locus_names names for each genomic locus represented by windows
#' @param offset offset to use for center of region, used when plotting multiple
#' regions
#' @param xtitle title for x axis
#' @param ... additional arguments from \code{\link{set_track_parameters}}
#' @param summary_args lof arguments to override from
#' \code{\link{set_summary_parameters}}
#' @export
#' @aliases plot_tracks,character-method plot_tracks,GenomicRanges-method
#' @author Alicia Schep and Justin Finkle
#' @rdname plot_tracks
#' @name plot_tracks
#' @return GenomeTrackWidgets object, which is displayed as htmlwidgets. To
#' convert manually to htmlwidgets, use to_widget
#'
#' @examples
#'
#' library(GenomicRanges)
#' library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#'
#' ## we'll read in some RNA counts
#' data(rpkm_chr21)
#'
#' ## From the ranges of the rpkm object, we'll pull out the tss
#' chr21_promoters <- promoters(SummarizedExperiment::rowRanges(rpkm_chr21),
#' up = 1000, down = 1000)
#'
#' ## set summary parameters
#'
#' summary_params <- set_summary_parameters(rpkm_chr21,
#' groups = "GROUP", ranges = chr21_promoters)
#'
#' ## We'll also read in some track data to plot
#' genomation_dir <- system.file("extdata", package = "genomationData")
#' samp.file <- file.path(genomation_dir,'SamplesInfo.txt')
#' samp.info <- read.table(samp.file, header=TRUE, sep="\t",
#' stringsAsFactors = FALSE)
#' samp.info$fileName <- file.path(genomation_dir, samp.info$fileName)
#'
#' ## Make track plotter using summary parametrs
#'
#' track_params <- set_track_parameters(samp.info$fileName[1:3],
#' annotation = TxDb.Hsapiens.UCSC.hg19.knownGene,
#' track_names = samp.info$sampleName[1:3],
#' share_y = TRUE,
#' summary = summary_params)
#'
#' if (interactive()){
#' plot_tracks(rownames(rpkm_chr21)[1:3], track_params)
#' plot(chr21_promoters[1:3], track_params)
#' }
#'
setMethod("plot_tracks", c("character"),
function(windows,
params,
locus_names = windows,
offset = NULL,
xtitle =
if (length(windows) > 1) "Relative Position"
else NULL,
...,
summary_args = list()){
if (is.null(params@summary)){
stop("params must include summary parameters for calling ",
"plot_tracks via a character vector")
}
ix <- match(windows, rownames(params@summary@data))
ranges <- params@summary@ranges[ix]
if (is.null(offset)){offset <- width(ranges[1]) %/% 2}
if (is.null(xtitle)){
if (length(windows) > 1){
xtitle <- ""
} else{
xtitle <- seqnames(ranges)
}
}
arglist <- modify_param_args(params, xtitle, offset, locus_names,
...)
tracks <- do.call(multi_locus_view,
c(list(windows = ranges), arglist))
if (any(is.na(ix))){
warning("Windows don't match ranges stored in TrackParameters ","
for summary. Not plotting summaries.")
} else{
summary_arglist <- modify_summary_args(params,summary_args)
summary_arglist[["row_names"]] <-
windows
summaries <- do.call(make_locus_summaries, summary_arglist)
out <- new("GenomeTrackWidget", tracks = tracks,
summaries = summaries,
summary_width = params@summary@width,
layout = arglist$layout)
}
out
})
modify_param_args <- function(params, xtitle, offset, locus_names, ...){
new_args <- list(...)
new_layout <- if ("layout" %in% names(new_args)){
modifyList(params@layout, new_args[["layout"]])
} else{
params@layout
}
default_arglist <- list(
object = params@data,
annotation = params@annotation,
track_names = params@track_names,
name = locus_names,
groups = params@groups,
share_y = params@share_y,
fill = params@fill,
showlegend = params@showlegend,
colors = params@colors,
mode = params@mode,
annotation_position = params@annotation_position,
annotation_size = params@annotation_size,
layout = new_layout,
offset = offset,
xtitle = xtitle
)
modifyList(default_arglist, new_args)
}
modify_summary_args <- function(params, summary_args){
default_summary_arglist <-
list(object = params@summary@data,
assay_name = params@summary@assay_name,
groups = params@summary@groups,
showlegend = params@summary@showlegend,
boxpoints = params@summary@boxpoints,
pointpos = params@summary@pointpos,
ytitle = params@summary@ytitle)
modifyList(default_summary_arglist,
summary_args)
}
skummerf/GenomicWidgets documentation built on May 31, 2019, 6:16 p.m.
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#' set_track_parameters
#'
#' Setup parameters for plotting coverage signals along genome tracks.
#' Result from this function can be passed to \code{\link{plot_tracks}}
#'
#' @param object vector of bam or bigwig file names
#' @param annotation TxDb or OrganismDb object
#' @param ... additional arguments
#' @param track_names names to associate with each file
#' @param groups vector of group assignments. traces will be grouped onto
#' subplots based on group assignments (if only showing 1 region)
#' @param share_y share the y axis?
#' @param fill fillmode for line plot
#' @param showlegend show the legend?
#' @param colors colors for each bam file
#' @param mode mode for plot
#' @param annotation_position plot annotations on bottom or on top of signal
#' traces
#' @param annotation_size relative size of annotation plot
#' @param summary Summary parameters from \code{\link{set_summary_parameters}}
#' @param layout list of additional plotly layout arguments
#' @export
#' @rdname set_track_parameters
#' @name set_track_parameters
#' @aliases set_track_parameters,character-method
#'
#' @author Alicia Schep and Justin Finkle
#' @return object storing track parameters, for use in \code{\link{plot_tracks}}
#' @examples
#'
#' library(GenomicRanges)
#' library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#'
#' ## First we'll read in some sample data
#' genomation_dir <- system.file("extdata", package = "genomationData")
#' samp.file <- file.path(genomation_dir,'SamplesInfo.txt')
#' samp.info <- read.table(samp.file, header=TRUE, sep="\t",
#' stringsAsFactors = FALSE)
#' samp.info$fileName <- file.path(genomation_dir, samp.info$fileName)
#' ctcf.peaks = genomation::readBroadPeak(system.file("extdata",
#' "wgEncodeBroadHistoneH1hescCtcfStdPk.broadPeak.gz",
#' package = "genomationData"))
#' ctcf.peaks = ctcf.peaks[seqnames(ctcf.peaks) == "chr21"]
#'
#' ## resize peaks to size 1000
#' ctcf.peaks = resize(ctcf.peaks, width = 10000, fix = "center")
#'
#' ## Make track plotter
#'
#' track_params <- set_track_parameters(samp.info$fileName[1:3],
#' annotation = TxDb.Hsapiens.UCSC.hg19.knownGene,
#' track_names = samp.info$sampleName[1:3] ,
#' share_y = TRUE)
#'
#' if (interactive()){
#' plot_tracks(ctcf.peaks[1], track_params)
#' plot(ctcf.peaks[1:3], track_params)
#' }
#'
setMethod("set_track_parameters", c("character"),
function(object,
annotation = NULL,
track_names = if (!is.null(names(object)))
names(object)
else basename(object),
groups = track_names,
share_y = TRUE,
showlegend = TRUE,
colors = NULL,
fill = c("tozeroy","none"),
mode = "lines",
annotation_position = c("bottom","top"),
annotation_size = 0.25,
summary = NULL,
layout = list()){
params <- list(Class = "TrackParameters",
data = object,
annotation = unpack_transcripts(annotation),
track_names = track_names,
groups = as.factor(groups),
summary = summary,
showlegend = showlegend,
share_y = share_y,
colors = select_colors(colors,length(object)),
fill = match.arg(fill),
annotation_position = match.arg(annotation_position),
mode = mode,
annotation_size = annotation_size,
layout = layout)
do.call(new, params)
})
#' set_summary_parameters
#'
#' Setup parameters for plotting summaries along genome tracks.
#' Result from this function can be passed to \code{\link{set_track_parameters}}
#'
#' @param object SummarizedExperiment
#' @param assay_name name of assay to use
#' @param ... additional arguments
#' @param groups either vector of group assignments of name of column in object
#' colData that corresponds to vector of group assignments
#' @param showlegend show the legend?
#' @param colors colors to use
#' @param boxpoints plot individual points?
#' @param pointpos relative position of points to boxes
#' @param ytitle name for yaxis
#' @param ranges ranges corresponding to rows of object
#' @param width relative width of summary plots when plotting tracks
#' @export
#' @return object storing summary parameters, for use in
#' \code{\link{set_track_parameters}}
#' @author Alicia Schep and Justin Finkle
#' @rdname set_summary_parameters
#' @name set_summary_parameters
#' @aliases set_summary_parameters,SummarizedExperiment-method
#' set_summary_parameters,RangedSummarizedExperiment-method
#' @examples
#'
#'
#' library(GenomicRanges)
#' library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#'
#' ## we'll read in some RNA counts
#' data(rpkm_chr21)
#'
#' ## From the ranges of the rpkm object, we'll pull out the tss
#' chr21_promoters <- promoters(SummarizedExperiment::rowRanges(rpkm_chr21),
#' up = 1000, down = 1000)
#'
#' ## set summary parameters
#'
#' summary_params <- set_summary_parameters(rpkm_chr21,
#' groups = "GROUP", ranges = chr21_promoters)
#'
#' ## We'll also read in some track data to plot
#' genomation_dir <- system.file("extdata", package = "genomationData")
#' samp.file <- file.path(genomation_dir,'SamplesInfo.txt')
#' samp.info <- read.table(samp.file, header=TRUE, sep="\t",
#' stringsAsFactors = FALSE)
#' samp.info$fileName <- file.path(genomation_dir, samp.info$fileName)
#'
#' ## Make track plotter using summary parametrs
#'
#' track_params <- set_track_parameters(samp.info$fileName[1:3],
#' annotation = TxDb.Hsapiens.UCSC.hg19.knownGene,
#' track_names = samp.info$sampleName[1:3],
#' share_y = TRUE,
#' summary = summary_params)
#'
#' if (interactive()){
#' plot_tracks(rownames(rpkm_chr21)[1:3], track_params)
#' plot(chr21_promoters[1:3], track_params)
#' }
#'
setMethod("set_summary_parameters", c("SummarizedExperiment"),
function(object,
ranges,
assay_name = assayNames(object)[1],
groups = colnames(object),
colors = "blue",
showlegend = length(colors) > 1,
boxpoints = c("all","Outliers","false"),
pointpos = 0,
ytitle = "Expression",
width = 0.3){
# Check groups
if (is.null(groups)){
groups <- ""
} else if (length(groups) == 1){
if (groups %in% colnames(colData(object)))
groups <- colData(object)[,groups]
} else{
stopifnot(length(groups) == ncol(object))
}
params <- list(Class = "SummaryParameters",
data = object,
assay_name = assay_name,
groups = groups,
colors = colors,
showlegend = showlegend,
boxpoints = match.arg(boxpoints),
pointpos = pointpos,
ytitle = ytitle,
width = width,
ranges = ranges
)
do.call(new, params)
})
#' @export
#' @rdname set_summary_parameters
setMethod("set_summary_parameters", c("RangedSummarizedExperiment"),
function(object,
ranges = rowRanges(object),
assay_name = assayNames(object)[1],
groups = NULL,
colors = "blue",
showlegend = length(colors) > 1,
boxpoints = c("all","Outliers","false"),
pointpos = 0,
ytitle = "Expression",
width = 0.3){
# Check groups
if (is.null(groups)){
groups <- ""
} else if (length(groups) == 1){
if (groups %in% colnames(colData(object)))
groups <- colData(object)[,groups]
} else{
stopifnot(length(groups) == ncol(object))
}
params <- list(Class = "SummaryParameters",
data = object,
assay_name = assay_name,
groups = groups,
colors = colors,
showlegend = showlegend,
boxpoints = match.arg(boxpoints),
pointpos = pointpos,
ytitle = ytitle,
width = width,
ranges = ranges
)
do.call(new, params)
})
#' @export
#' @rdname plot_tracks
setMethod("plot_tracks", c("GenomicRanges"),
function(windows,
params,
locus_names = mcols(windows)$name,
offset = width(windows[1]) %/% 2,
xtitle =
if (length(windows) > 1) "Relative Position"
else seqnames(windows),
...,
summary_args = list()){
arglist <- modify_param_args(params, xtitle, offset, locus_names,
...)
tracks <- do.call(multi_locus_view,
c(list(windows = windows), arglist))
out <- new("GenomeTrackWidget",
tracks = tracks,
summary_width = 0,
layout = arglist$layout)
if (!is.null(params@summary)){
ix <- match(windows, params@summary@ranges)
if (any(is.na(ix))){
warning("Windows don't match ranges stored in TrackParameters ",
"for summary. Not plotting summaries.")
} else{
summary_arglist <- modify_summary_args(params,summary_args)
summary_arglist[["row_names"]] <-
rownames(params@summary@data)[ix]
summaries <- do.call(make_locus_summaries, summary_arglist)
out <- new("GenomeTrackWidget",
tracks = tracks,
summaries = summaries,
summary_width = params@summary@width,
layout = arglist$layout)
}
} else{
out <- new("GenomeTrackWidget",
tracks = tracks,
summary_width = 0,
layout = arglist$layout)
}
out
})
#' plot_tracks
#'
#' @param windows GenomicRanges or rownames for summary object
#' @param params TrackParameters, from \code{\link{set_track_parameters}}
#' @param locus_names names for each genomic locus represented by windows
#' @param offset offset to use for center of region, used when plotting multiple
#' regions
#' @param xtitle title for x axis
#' @param ... additional arguments from \code{\link{set_track_parameters}}
#' @param summary_args lof arguments to override from
#' \code{\link{set_summary_parameters}}
#' @export
#' @aliases plot_tracks,character-method plot_tracks,GenomicRanges-method
#' @author Alicia Schep and Justin Finkle
#' @rdname plot_tracks
#' @name plot_tracks
#' @return GenomeTrackWidgets object, which is displayed as htmlwidgets. To
#' convert manually to htmlwidgets, use to_widget
#'
#' @examples
#'
#' library(GenomicRanges)
#' library(TxDb.Hsapiens.UCSC.hg19.knownGene)
#'
#' ## we'll read in some RNA counts
#' data(rpkm_chr21)
#'
#' ## From the ranges of the rpkm object, we'll pull out the tss
#' chr21_promoters <- promoters(SummarizedExperiment::rowRanges(rpkm_chr21),
#' up = 1000, down = 1000)
#'
#' ## set summary parameters
#'
#' summary_params <- set_summary_parameters(rpkm_chr21,
#' groups = "GROUP", ranges = chr21_promoters)
#'
#' ## We'll also read in some track data to plot
#' genomation_dir <- system.file("extdata", package = "genomationData")
#' samp.file <- file.path(genomation_dir,'SamplesInfo.txt')
#' samp.info <- read.table(samp.file, header=TRUE, sep="\t",
#' stringsAsFactors = FALSE)
#' samp.info$fileName <- file.path(genomation_dir, samp.info$fileName)
#'
#' ## Make track plotter using summary parametrs
#'
#' track_params <- set_track_parameters(samp.info$fileName[1:3],
#' annotation = TxDb.Hsapiens.UCSC.hg19.knownGene,
#' track_names = samp.info$sampleName[1:3],
#' share_y = TRUE,
#' summary = summary_params)
#'
#' if (interactive()){
#' plot_tracks(rownames(rpkm_chr21)[1:3], track_params)
#' plot(chr21_promoters[1:3], track_params)
#' }
#'
setMethod("plot_tracks", c("character"),
function(windows,
params,
locus_names = windows,
offset = NULL,
xtitle =
if (length(windows) > 1) "Relative Position"
else NULL,
...,
summary_args = list()){
if (is.null(params@summary)){
stop("params must include summary parameters for calling ",
"plot_tracks via a character vector")
}
ix <- match(windows, rownames(params@summary@data))
ranges <- params@summary@ranges[ix]
if (is.null(offset)){offset <- width(ranges[1]) %/% 2}
if (is.null(xtitle)){
if (length(windows) > 1){
xtitle <- ""
} else{
xtitle <- seqnames(ranges)
}
}
arglist <- modify_param_args(params, xtitle, offset, locus_names,
...)
tracks <- do.call(multi_locus_view,
c(list(windows = ranges), arglist))
if (any(is.na(ix))){
warning("Windows don't match ranges stored in TrackParameters ","
for summary. Not plotting summaries.")
} else{
summary_arglist <- modify_summary_args(params,summary_args)
summary_arglist[["row_names"]] <-
windows
summaries <- do.call(make_locus_summaries, summary_arglist)
out <- new("GenomeTrackWidget", tracks = tracks,
summaries = summaries,
summary_width = params@summary@width,
layout = arglist$layout)
}
out
})
modify_param_args <- function(params, xtitle, offset, locus_names, ...){
new_args <- list(...)
new_layout <- if ("layout" %in% names(new_args)){
modifyList(params@layout, new_args[["layout"]])
} else{
params@layout
}
default_arglist <- list(
object = params@data,
annotation = params@annotation,
track_names = params@track_names,
name = locus_names,
groups = params@groups,
share_y = params@share_y,
fill = params@fill,
showlegend = params@showlegend,
colors = params@colors,
mode = params@mode,
annotation_position = params@annotation_position,
annotation_size = params@annotation_size,
layout = new_layout,
offset = offset,
xtitle = xtitle
)
modifyList(default_arglist, new_args)
}
modify_summary_args <- function(params, summary_args){
default_summary_arglist <-
list(object = params@summary@data,
assay_name = params@summary@assay_name,
groups = params@summary@groups,
showlegend = params@summary@showlegend,
boxpoints = params@summary@boxpoints,
pointpos = params@summary@pointpos,
ytitle = params@summary@ytitle)
modifyList(default_summary_arglist,
summary_args)
}
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