Nothing
R/plotAverage.R
In seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
#' Create the average plot
#'
#' Draw an average plot from \code{\link{PlotSetArray}},
#' \code{\link{PlotSetList}}, \code{\link{PlotSetPair}} or properly formatted
#' \code{\link[base]{list}} in active graphics window. Axes and titles, keys and
#' other plot elements are controlled by function parameters.
#'
#'
#' @param plotset The dataset to plot - can be \code{\link{PlotSetArray}},
#' \code{\link{PlotSetList}}, \code{\link{PlotSetPair}} or properly formated
#' \code{\link[base]{list}}
#' @param main The main title of the plot, shown in top-centred part of the
#' figure; defaults to NULL (not visible)
#' @param xlab Label shown below horizontal axis; default to \code{""} (empty)
#' @param ylab Label shown below vertical axis; default to \code{""} (empty)
#' @param labels The character vector giving labels used in experiment key. The
#' defaults NULL value indicates taht feature/track file names will be used to
#' generate the labels.
#' @param keepratio If TRUE keep 1:1 aspect ratio of the figure; defaults to
#' FALSE
#' @param plotScale scale the available data before plotting, can be "linear"
#' (do not scale, default), "log2" or "zscore"
#' @param xlim the x limits (x1, x2) of the plot. Note that x1 > x2 is allowed
#' and leads to a "reversed axis". The default value, NULL, indicates that the
#' whole range present in \code{plotset} will be plotted.
#' @param ylim the y limits (y1, y2) of the plot. Note that x1 > x2 is allowed
#' and leads to a "reversed axis". The default value, NULL, indicates that the
#' range will be auto calculated including space for error estimates.
#' @param type If set to "legend" only the legend/key will be plotted.
#' @param error.estimates Indicates if error estimates are plotted, defaults to
#' TRUE
#' @param legend Indicates if key describing the PlotSetPairs is shown, defaults
#' to TRUE
#' @param legend_ext Indicates if key describing error estimates is shown,
#' defaults to FALSE
#' @param legend_pos The position of main key, defaults to 'topright'
#' @param legend_ext_pos The position of error estimates key, defaults to
#' 'topleft'
#' @param cex.axis Axis numbers font size in points, defaults to 14
#' @param cex.lab Axis labels font size in points, Defaults to 16
#' @param cex.main Main title font size in points, defaults to 20
#' @param cex.legend Keys labels font size in points, defaults to 10
#' @param ln.v Determins if vertical guide line(s) should be plotted (TRUE) or
#' ommitted (FALSE). For anchored plots 2 lines indicating the start and end
#' of anchored distane are plotted.
#' @param ln.h Determins if horizontal guide line should is plotted. Numeric
#' value of the parameter indicates the Y-axis position of the lie, NULL
#' (default) indicates to omit
#' @param colvec The vector of colours used to plot the lines and error estimate
#' fields. If set value NULL (default) the automatically generated colour
#' values will be used. Accpeted values are: vector of any of the three kinds
#' of R colour specifications, i.e., either a colour name (as listed by
#' colors()), a hexadecimal string of the form "#rrggbb" or "#rrggbbaa" (see
#' rgb), or a positive integer i meaning palette()[i]. See
#' \code{\link[grDevices]{col2rgb}}.
#' @param pointsize The default font point size to be used for plots. Defaults
#' to 12 (1/72 inch).
#' @param ... other graphical parameters passed to plot.default (see
#' \code{\link[graphics]{plot.default}}, \code{\link[graphics]{par}} and
#' section "Details" below)
#'
#'
#' @return \code{NULL}
#'
#' @details Relevant parameters passed to \code{\link[graphics]{plot.default}}
#' function: \describe{ \item{\code{log}}{a character string which contains "x"
#' if the x axis is to be logarithmic, "y" if the y axis is to be logarithmic
#' and "xy" or "yx" if both axes are to be logarithmic.} \item{\code{ann}}{a
#' logical value indicating whether the default annotation (title and x and y
#' axis labels) should appear on the plot.} \item{\code{axes}}{a logical value
#' indicating whether both axes should be drawn on the plot. Use graphical
#' parameter "xaxt" or "yaxt" to suppress just one of the axes.}
#' \item{\code{rame.plot}}{a logical indicating whether a box should be drawn
#' around the plot.} \item{\code{panel.first}}{an "expression" to be evaluated
#' after the plot axes are set up but before any plotting takes place. This can
#' be useful for drawing background grids or scatterplot smooths. Note that this
#' works by lazy evaluation: passing this argument from other plot methods may
#' well not work since it may be evaluated too early.}
#' \item{\code{panel.last}}{an expression to be evaluated after plotting has
#' taken place but before the axes, title and box are added. See the comments
#' about panel.first.} \item{\code{asp}}{the y/x aspect ratio, see plot.window.}
#' }
#'
#' @author Przemyslaw Stempor
#'
#' @family plotting functions
#' @export
#'
#' @examples
#' # Get the paths of example files
#' bed1 <- system.file("extdata",
#' "Transcripts_ce10_chrI_100Kb.bed", package="seqplots")
#' bed2 <- system.file("extdata",
#' "GSM1208361_chrI_100Kb_PeakCalls.bed", package="seqplots")
#' bw1 <- system.file("extdata",
#' "GSM1208360_chrI_100Kb_q5_sample.bw", package="seqplots")
#'
#' #If required install C. elegans genomic package from Bioconductor
#' if(!"BSgenome.Celegans.UCSC.ce10" %in% BSgenome::installed.genomes()) {
#' if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
#' if (!requireNamespace("BiocManager", quietly=TRUE))
#' install.packages("BiocManager")
#' BiocManager::install("BSgenome.Celegans.UCSC.ce10")
#' }
#' }
#'
#' #Get getPlotSetArray for track and feature files
#' if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
#' plotset1 <- getPlotSetArray(bw1, c(bed1, bed2), 'ce10')
#' } else {
#' load(system.file("extdata", "precalc_plotset.Rdata", package="seqplots"))
#' }
#'
#' plotAverage(plotset1) # equivalent to plot(plotset1) or plotset1$plot()
#'
#'
setGeneric(
"plotAverage",
function(
plotset, keepratio=FALSE, labels=NULL, xlim=NULL, ylim=NULL,
main=NULL, xlab='', ylab='', plotScale='linear', type='full',
error.estimates=TRUE, legend=TRUE, legend_ext=FALSE,
legend_pos='topright', legend_ext_pos="topleft", cex.axis=14,
cex.lab=16, cex.main=20, cex.legend=10, ln.v=TRUE, ln.h=NULL,
colvec=NULL, pointsize=12, ...
) {
standardGeneric("plotAverage")
}
)
#' @describeIn plotAverage Method for signature plotset='list'
setMethod(
"plotAverage", signature(plotset='list'),
function(plotset, ...) {
opar <- par(no.readonly = TRUE)['pty']
if(keepratio) par(pty='s')
if( length(labels) ) {
labels <- labels[1:length(plotset)]
plotset <- Map(function(x, y) {
if(!is.na(y)) x[['desc']]<-y; return(x)
}, plotset, labels)
}
plotMext(
plotset, xlim=xlim, ylim=ylim, main=main, xlab=xlab, ylab=ylab,
plotScale=plotScale, type=type, error.estimates=error.estimates,
legend=legend, legend_ext=legend_ext, legend_pos=legend_pos,
legend_ext_pos=legend_ext_pos, cex.axis=cex.axis, cex.lab=cex.lab,
cex.main=cex.main, cex.legend=cex.legend, ln.v=ln.v, ln.h=ln.h,
colvec=colvec, pointsize=pointsize, ...
)
par(opar)
return(invisible(NULL))
}
)
#' @describeIn plotAverage Method for signature plotset='PlotSetPair'
#' @include PlotSetPair-class.R
setMethod(
"plotAverage", signature(plotset='PlotSetPair'),
function(plotset, ...) {
plotAverage(
list(plotset), keepratio, labels, xlim, ylim, main,
xlab, ylab, plotScale, type, error.estimates, legend, legend_ext,
legend_pos, legend_ext_pos, cex.axis, cex.lab, cex.main,
cex.legend, ln.v, ln.h, colvec, pointsize, ...
)
}
)
#' @describeIn plotAverage Method for signature plotset='PlotSetList'
#' @include PlotSetList-class.R
setMethod(
"plotAverage", signature(plotset='PlotSetList'),
function(plotset, ...) {
plotAverage(
plotset$data, keepratio, labels, xlim, ylim, main, xlab, ylab,
plotScale, type, error.estimates, legend, legend_ext, legend_pos,
legend_ext_pos, cex.axis, cex.lab, cex.main, cex.legend, ln.v,
ln.h, colvec, pointsize, ...
)
}
)
#' @describeIn plotAverage Method for signature plotset='PlotSetArray'
#' @include PlotSetArray-class.R
setMethod(
"plotAverage", signature(plotset='PlotSetArray'),
function(plotset, ...) {
plotAverage(
plotset$unlist()$data, keepratio, labels, xlim, ylim, main,
xlab, ylab, plotScale, type, error.estimates, legend, legend_ext,
legend_pos, legend_ext_pos, cex.axis, cex.lab, cex.main,
cex.legend, ln.v, ln.h, colvec, pointsize, ...
)
}
)
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#' Create the average plot
#'
#' Draw an average plot from \code{\link{PlotSetArray}},
#' \code{\link{PlotSetList}}, \code{\link{PlotSetPair}} or properly formatted
#' \code{\link[base]{list}} in active graphics window. Axes and titles, keys and
#' other plot elements are controlled by function parameters.
#'
#'
#' @param plotset The dataset to plot - can be \code{\link{PlotSetArray}},
#' \code{\link{PlotSetList}}, \code{\link{PlotSetPair}} or properly formated
#' \code{\link[base]{list}}
#' @param main The main title of the plot, shown in top-centred part of the
#' figure; defaults to NULL (not visible)
#' @param xlab Label shown below horizontal axis; default to \code{""} (empty)
#' @param ylab Label shown below vertical axis; default to \code{""} (empty)
#' @param labels The character vector giving labels used in experiment key. The
#' defaults NULL value indicates taht feature/track file names will be used to
#' generate the labels.
#' @param keepratio If TRUE keep 1:1 aspect ratio of the figure; defaults to
#' FALSE
#' @param plotScale scale the available data before plotting, can be "linear"
#' (do not scale, default), "log2" or "zscore"
#' @param xlim the x limits (x1, x2) of the plot. Note that x1 > x2 is allowed
#' and leads to a "reversed axis". The default value, NULL, indicates that the
#' whole range present in \code{plotset} will be plotted.
#' @param ylim the y limits (y1, y2) of the plot. Note that x1 > x2 is allowed
#' and leads to a "reversed axis". The default value, NULL, indicates that the
#' range will be auto calculated including space for error estimates.
#' @param type If set to "legend" only the legend/key will be plotted.
#' @param error.estimates Indicates if error estimates are plotted, defaults to
#' TRUE
#' @param legend Indicates if key describing the PlotSetPairs is shown, defaults
#' to TRUE
#' @param legend_ext Indicates if key describing error estimates is shown,
#' defaults to FALSE
#' @param legend_pos The position of main key, defaults to 'topright'
#' @param legend_ext_pos The position of error estimates key, defaults to
#' 'topleft'
#' @param cex.axis Axis numbers font size in points, defaults to 14
#' @param cex.lab Axis labels font size in points, Defaults to 16
#' @param cex.main Main title font size in points, defaults to 20
#' @param cex.legend Keys labels font size in points, defaults to 10
#' @param ln.v Determins if vertical guide line(s) should be plotted (TRUE) or
#' ommitted (FALSE). For anchored plots 2 lines indicating the start and end
#' of anchored distane are plotted.
#' @param ln.h Determins if horizontal guide line should is plotted. Numeric
#' value of the parameter indicates the Y-axis position of the lie, NULL
#' (default) indicates to omit
#' @param colvec The vector of colours used to plot the lines and error estimate
#' fields. If set value NULL (default) the automatically generated colour
#' values will be used. Accpeted values are: vector of any of the three kinds
#' of R colour specifications, i.e., either a colour name (as listed by
#' colors()), a hexadecimal string of the form "#rrggbb" or "#rrggbbaa" (see
#' rgb), or a positive integer i meaning palette()[i]. See
#' \code{\link[grDevices]{col2rgb}}.
#' @param pointsize The default font point size to be used for plots. Defaults
#' to 12 (1/72 inch).
#' @param ... other graphical parameters passed to plot.default (see
#' \code{\link[graphics]{plot.default}}, \code{\link[graphics]{par}} and
#' section "Details" below)
#'
#'
#' @return \code{NULL}
#'
#' @details Relevant parameters passed to \code{\link[graphics]{plot.default}}
#' function: \describe{ \item{\code{log}}{a character string which contains "x"
#' if the x axis is to be logarithmic, "y" if the y axis is to be logarithmic
#' and "xy" or "yx" if both axes are to be logarithmic.} \item{\code{ann}}{a
#' logical value indicating whether the default annotation (title and x and y
#' axis labels) should appear on the plot.} \item{\code{axes}}{a logical value
#' indicating whether both axes should be drawn on the plot. Use graphical
#' parameter "xaxt" or "yaxt" to suppress just one of the axes.}
#' \item{\code{rame.plot}}{a logical indicating whether a box should be drawn
#' around the plot.} \item{\code{panel.first}}{an "expression" to be evaluated
#' after the plot axes are set up but before any plotting takes place. This can
#' be useful for drawing background grids or scatterplot smooths. Note that this
#' works by lazy evaluation: passing this argument from other plot methods may
#' well not work since it may be evaluated too early.}
#' \item{\code{panel.last}}{an expression to be evaluated after plotting has
#' taken place but before the axes, title and box are added. See the comments
#' about panel.first.} \item{\code{asp}}{the y/x aspect ratio, see plot.window.}
#' }
#'
#' @author Przemyslaw Stempor
#'
#' @family plotting functions
#' @export
#'
#' @examples
#' # Get the paths of example files
#' bed1 <- system.file("extdata",
#' "Transcripts_ce10_chrI_100Kb.bed", package="seqplots")
#' bed2 <- system.file("extdata",
#' "GSM1208361_chrI_100Kb_PeakCalls.bed", package="seqplots")
#' bw1 <- system.file("extdata",
#' "GSM1208360_chrI_100Kb_q5_sample.bw", package="seqplots")
#'
#' #If required install C. elegans genomic package from Bioconductor
#' if(!"BSgenome.Celegans.UCSC.ce10" %in% BSgenome::installed.genomes()) {
#' if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
#' if (!requireNamespace("BiocManager", quietly=TRUE))
#' install.packages("BiocManager")
#' BiocManager::install("BSgenome.Celegans.UCSC.ce10")
#' }
#' }
#'
#' #Get getPlotSetArray for track and feature files
#' if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
#' plotset1 <- getPlotSetArray(bw1, c(bed1, bed2), 'ce10')
#' } else {
#' load(system.file("extdata", "precalc_plotset.Rdata", package="seqplots"))
#' }
#'
#' plotAverage(plotset1) # equivalent to plot(plotset1) or plotset1$plot()
#'
#'
setGeneric(
"plotAverage",
function(
plotset, keepratio=FALSE, labels=NULL, xlim=NULL, ylim=NULL,
main=NULL, xlab='', ylab='', plotScale='linear', type='full',
error.estimates=TRUE, legend=TRUE, legend_ext=FALSE,
legend_pos='topright', legend_ext_pos="topleft", cex.axis=14,
cex.lab=16, cex.main=20, cex.legend=10, ln.v=TRUE, ln.h=NULL,
colvec=NULL, pointsize=12, ...
) {
standardGeneric("plotAverage")
}
)
#' @describeIn plotAverage Method for signature plotset='list'
setMethod(
"plotAverage", signature(plotset='list'),
function(plotset, ...) {
opar <- par(no.readonly = TRUE)['pty']
if(keepratio) par(pty='s')
if( length(labels) ) {
labels <- labels[1:length(plotset)]
plotset <- Map(function(x, y) {
if(!is.na(y)) x[['desc']]<-y; return(x)
}, plotset, labels)
}
plotMext(
plotset, xlim=xlim, ylim=ylim, main=main, xlab=xlab, ylab=ylab,
plotScale=plotScale, type=type, error.estimates=error.estimates,
legend=legend, legend_ext=legend_ext, legend_pos=legend_pos,
legend_ext_pos=legend_ext_pos, cex.axis=cex.axis, cex.lab=cex.lab,
cex.main=cex.main, cex.legend=cex.legend, ln.v=ln.v, ln.h=ln.h,
colvec=colvec, pointsize=pointsize, ...
)
par(opar)
return(invisible(NULL))
}
)
#' @describeIn plotAverage Method for signature plotset='PlotSetPair'
#' @include PlotSetPair-class.R
setMethod(
"plotAverage", signature(plotset='PlotSetPair'),
function(plotset, ...) {
plotAverage(
list(plotset), keepratio, labels, xlim, ylim, main,
xlab, ylab, plotScale, type, error.estimates, legend, legend_ext,
legend_pos, legend_ext_pos, cex.axis, cex.lab, cex.main,
cex.legend, ln.v, ln.h, colvec, pointsize, ...
)
}
)
#' @describeIn plotAverage Method for signature plotset='PlotSetList'
#' @include PlotSetList-class.R
setMethod(
"plotAverage", signature(plotset='PlotSetList'),
function(plotset, ...) {
plotAverage(
plotset$data, keepratio, labels, xlim, ylim, main, xlab, ylab,
plotScale, type, error.estimates, legend, legend_ext, legend_pos,
legend_ext_pos, cex.axis, cex.lab, cex.main, cex.legend, ln.v,
ln.h, colvec, pointsize, ...
)
}
)
#' @describeIn plotAverage Method for signature plotset='PlotSetArray'
#' @include PlotSetArray-class.R
setMethod(
"plotAverage", signature(plotset='PlotSetArray'),
function(plotset, ...) {
plotAverage(
plotset$unlist()$data, keepratio, labels, xlim, ylim, main,
xlab, ylab, plotScale, type, error.estimates, legend, legend_ext,
legend_pos, legend_ext_pos, cex.axis, cex.lab, cex.main,
cex.legend, ln.v, ln.h, colvec, pointsize, ...
)
}
)
Try the seqplots package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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