R/plotTagMatrix.R
In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Defines functions
plotAvgProf.internal
plotAvgProf
plotPeakProf
Documented in
plotAvgProf
plotPeakProf
##' plot the profile of peaks
##'`
##' \code{plotPeakProf_MultiWindows()} is almost the same as \code{plotPeakProf2()}, having
##' the main difference of accepting two or more granges objects. Accepting more
##' granges objects can help compare the same peaks in different windows.
##'
##' \code{TxDb} parameter can accept txdb object.
##' But many regions can not be obtained by txdb object. In this case,
##' Users can provide self-made granges served the same role
##' as txdb object and pass to \code{TxDb} object.
##'
##' \code{by} the features of interest.
##'
##' (1) if users use \code{txdb}, \code{by} can be one of 'gene', 'transcript', 'exon',
##' 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.
##'
##' (2) if users use self-made granges object, \code{by} can be everything. Because this \code{by}
##' will not pass to functions to get features, which is different from the case of using
##' txdb object. This \code{by} is only used to made labels showed in picture.
##'
##' \code{type} means the property of the region. one of the "start site",
##' "end site" and "body".
##'
##' \code{upstream} and \code{downstream} parameter have different usages:
##'
##' (1) if \code{type == 'body'}, \code{upstream} and \code{downstream} can use to extend
##' the flank of body region.
##'
##' (2) if \code{type == 'start_site'/'end_site'}, \code{upstream} and \code{downstream} refer to
##' the upstream and downstream of the start_site or the end_site.
##'
##' \code{weightCol} refers to column in peak file. This column acts as a weight value. Details
##' see \url{https://github.com/YuLab-SMU/ChIPseeker/issues/15}
##'
##' \code{nbin} refers to the number of bins. \code{getTagMatrix()} provide a binning method
##' to get the tag matrix.
##'
##' There are two ways input a list of window.
##'
##' (1) Users can input a list of self-made granges objects
##'
##' (2) Users can input a list of \code{by} and only one \code{type}. In this way,
##' \code{plotPeakProf_MultiWindows()} can made a list of window from txdb object based on \code{by} and \code{type}.
##'
##' Warning:
##'
##' (1) All of these window should be the same type. It means users can only
##' compare a list of "start site"/"end site"/"body region" with the same upstream
##' and downstream.
##'
##' (2) So it will be only one \code{type} and several \code{by}.
##'
##' (3) Users can make window by txdb object or self-made granges object. Users can only
##' choose one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR' or 'UTR' in the
##' way of using txdb object. User can input any \code{by} in the way of using
##' self-made granges object.
##'
##' (4) Users can mingle the \code{by} designed for the two ways. \code{plotPeakProf_MultiWindows} can
##' accpet the hybrid \code{by}. But the above rules should be followed.
##'
##' \url{https://github.com/YuLab-SMU/ChIPseeker/issues/189}
##'
##' @title plotPeakProf_MultiWindows
##'
##' @param tagMatrix tagMatrix or a list of tagMatrix
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object or self-made granges objects
##' @param upstream upstream position
##' @param downstream downstream position
##' @param by feature of interest
##' @param type one of "start_site", "end_site", "body"
##' @param windows_name the name for each window, which will also be showed in the picture as labels
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param verbose print message or not
##' @param nbin the amount of bines
##' @param ignore_strand ignore the strand information or not
##' @param ... additional parameter
##' @return ggplot object
##' @importFrom methods is
##' @importFrom methods as
##' @importFrom methods missingArg
##' @importFrom methods new
##' @export
plotPeakProf <- function(tagMatrix = NULL,
peak,
upstream,
downstream,
conf,
by,
type,
windows_name = NULL,
weightCol = NULL,
TxDb = NULL,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet = "row",
free_y = TRUE,
verbose = TRUE,
nbin = NULL,
ignore_strand = FALSE,
...){
if(is.null(tagMatrix)){
conf <- if(missingArg(conf)) NA else conf
upstream <- if(missingArg(upstream)) NULL else upstream
downstream <- if(missingArg(downstream)) NULL else downstream
if(length(by) == 1){
plotPeakProf2(peak = peak,
upstream = upstream,
downstream = downstream,
conf = conf,
by = by,
type = type,
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
nbin = nbin,
ignore_strand = ignore_strand,
...)
}else{
if(is.null(windows_name) && !is.null(names(TxDb)))
windows_name <- names(TxDb)
plotPeakProf_MultiWindows(peak = peak,
upstream = upstream,
downstream = downstream,
conf = conf,
by = by,
type = type,
windows_name = windows_name,
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
nbin = nbin,
ignore_strand = ignore_strand,
...)
}
}else{
if(is(tagMatrix, "list")){
upstream <- attr(tagMatrix[[1]], 'upstream')
downstream <- attr(tagMatrix[[1]], 'downstream')
label <- attr(tagMatrix[[1]], 'label')
attr(tagMatrix, 'type') <- attr(tagMatrix[[1]], 'type')
attr(tagMatrix, 'is.binning') <- attr(tagMatrix[[1]], 'is.binning')
}else{
upstream <- attr(tagMatrix, 'upstream')
downstream <- attr(tagMatrix, 'downstream')
label <- attr(tagMatrix, 'label')
}
if(attr(tagMatrix, 'is.binning')){
if (!(missingArg(conf) || is.na(conf))){
plotAvgProf.binning(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
conf = conf,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}else{
plotAvgProf.binning(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}
}else{
xlim <- c(-upstream, downstream)
if (!(missingArg(conf) || is.na(conf))){
plotAvgProf (tagMatrix = tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
conf = conf,
facet = facet,
free_y = free_y,
origin_label = label,
...)
}else{
plotAvgProf (tagMatrix = tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = label,
...)
}
}
}
}
##' plot the profile of peaks
##'
##'
##' @title plotAvgProf
##' @param tagMatrix tagMatrix or a list of tagMatrix
##' @param xlim xlim
##' @param xlab x label
##' @param ylab y label
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param origin_label label of the center
##' @param verbose print message or not
##' @param ... additional parameter
##' @return ggplot object
##' @author G Yu; Y Yan
##' @export
plotAvgProf <- function(tagMatrix, xlim,
xlab="Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet="none",
free_y = TRUE,
origin_label = "TSS",
verbose = TRUE,
...) {
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
if (verbose) {
cat(">> plotting figure...\t\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
conf <- if(missingArg(conf)) NA else conf
if (!(missingArg(conf) || is.na(conf))){
p <- plotAvgProf.internal(tagMatrix = tagMatrix,
conf = conf,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = origin_label,
...)
} else {
p <- plotAvgProf.internal(tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = origin_label,
...)
}
return(p)
}
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 geom_line
##' @importFrom ggplot2 geom_vline
##' @importFrom ggplot2 geom_ribbon
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 scale_color_manual
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 theme_bw
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 facet_grid
plotAvgProf.internal <- function(tagMatrix, conf,
xlim = c(-3000,3000),
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="none",
free_y = TRUE,
origin_label,
...) {
listFlag <- FALSE
if (is(tagMatrix, "list")) {
if ( is.null(names(tagMatrix)) ) {
nn <- paste0("peak", seq_along(tagMatrix))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(tagMatrix) <- nn
## stop("tagMatrix should be a named list...")
}
listFlag <- TRUE
}
if ( listFlag ) {
facet <- match.arg(facet, c("none", "row", "column"))
if ( (xlim[2]-xlim[1]+1) != ncol(tagMatrix[[1]]) ) {
stop("please specify appropreate xcoordinations...")
}
} else {
if ( (xlim[2]-xlim[1]+1) != ncol(tagMatrix) ) {
stop("please specify appropreate xcoordinations...")
}
}
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
##
conf <- if(missingArg(conf)) NA else conf
pos <- value <- .id <- Lower <- Upper <- NULL
if ( listFlag ) {
tagCount <- lapply(tagMatrix, function(x) getTagCount(x, xlim = xlim, conf = conf, ...))
tagCount <- list_to_dataframe(tagCount)
tagCount$.id <- factor(tagCount$.id, levels=names(tagMatrix))
p <- ggplot(tagCount, aes(pos, group=.id, color=.id))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = .id),
linetype = 0, alpha = 0.2)
}
} else {
tagCount <- getTagCount(tagMatrix, xlim = xlim, conf = conf, ...)
p <- ggplot(tagCount, aes(pos))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper),
linetype = 0, alpha = 0.2)
}
}
p <- p + geom_line(aes(y = value))
if ( 0 > xlim[1] && 0 < xlim[2] ) {
p <- p + geom_vline(xintercept=0,
linetype="longdash")
p <- p + scale_x_continuous(breaks=c(xlim[1], floor(xlim[1]/2),
0,
floor(xlim[2]/2), xlim[2]),
labels=c(paste0(xlim[1],"bp"), paste0(floor(xlim[1]/2),"bp"),
origin_label,
paste0(floor(xlim[2]/2),"bp"), paste0(xlim[2], "bp")))
}
if (listFlag) {
cols <- getCols(length(tagMatrix))
p <- p + scale_color_manual(values=cols)
if (facet == "row") {
if (free_y) {
p <- p + facet_grid(.id ~ ., scales = "free_y")
} else {
p <- p + facet_grid(.id ~ .)
}
} else if (facet == "column") {
if (free_y) {
p <- p + facet_grid(. ~ .id, scales = "free_y")
} else {
p <- p + facet_grid(. ~ .id)
}
}
}
p <- p+xlab(xlab)+ylab(ylab)
p <- p + theme_bw() + theme(legend.title=element_blank())
if(facet != "none") {
p <- p + theme(legend.position="none")
}
return(p)
}
##' plot the profile of peaks that align to flank sequences of TSS
##'
##' This function is the old function of \code{plotPeakProf2}. It can
##' only plot the start site region of gene.
##'
##' @title plotAvgProf
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param verbose print message or not
##' @param ignore_strand ignore the strand information or not
##' @param ... additional parameter
##' @return ggplot object
##' @export
##' @author G Yu, Ming L
plotAvgProf2 <- function(peak, weightCol = NULL, TxDb = NULL,
upstream = 1000, downstream = 1000,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet = "none",
free_y = TRUE,
verbose = TRUE,
ignore_strand = FALSE,
...) {
plotPeakProf2(peak = peak,
upstream = upstream,
downstream = downstream,
conf,
by = "gene",
type = "start_site",
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
ignore_strand = ignore_strand,
...)
}
##' plot the profile of peaks by binning
##'
##'
##' @title plotAvgProf.binning
##' @param tagMatrix tagMatrix or a list of tagMatrix
##' @param xlab x label
##' @param ylab y label
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled
##' @param upstream rel object reflects the percentage of flank extension, e.g rel(0.2)
##' integer reflects the actual length of flank extension or TSS region
##' NULL reflects the gene body with no extension
##' @param downstream rel object reflects the percentage of flank extension, e.g rel(0.2)
##' integer reflects the actual length of flank extension or TSS region
##' NULL reflects the gene body with no extension
##' @param label label
##' @param ... additional parameter
##' @return ggplot object
##' @importFrom ggplot2 rel
plotAvgProf.binning <- function(tagMatrix,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet ="none",
free_y = TRUE,
upstream = NULL,
downstream = NULL,
label,
...) {
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
conf <- if(missingArg(conf)) NA else conf
if (!(missingArg(conf) || is.na(conf))){
p <- plotAvgProf.binning.internal(tagMatrix ,
conf = conf,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
} else {
p <- plotAvgProf.binning.internal(tagMatrix ,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}
return(p)
}
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 geom_line
##' @importFrom ggplot2 geom_vline
##' @importFrom ggplot2 geom_ribbon
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 scale_color_manual
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 theme_bw
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 facet_grid
##' @importFrom ggplot2 rel
plotAvgProf.binning.internal <- function(tagMatrix,
conf,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="none",
free_y = TRUE,
upstream = NULL,
downstream = NULL,
label,
...) {
listFlag <- FALSE
if (is(tagMatrix, "list")) {
if ( is.null(names(tagMatrix )) ) {
nn <- paste0("peak", seq_along(tagMatrix ))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(tagMatrix) <- nn
## stop("tagMatrix should be a named list...")
}
listFlag <- TRUE
}
if(listFlag){
nbin <- dim(tagMatrix[[1]])[2]
}else{
nbin <- dim(tagMatrix)[2]
}
xlim <- c(1,nbin)
if ( listFlag ) {
facet <- match.arg(facet, c("none", "row", "column"))
}
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
##
conf <- if(missingArg(conf)) NA else conf
pos <- value <- .id <- Lower <- Upper <- NULL
if ( listFlag ) {
tagCount <- lapply(tagMatrix , function(x) getTagCount(x, xlim = xlim, conf = conf, ...))
tagCount <- list_to_dataframe(tagCount)
tagCount$.id <- factor(tagCount$.id, levels=names(tagMatrix ))
p <- ggplot(tagCount, aes(pos, group=.id, color=.id))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = .id),
linetype = 0, alpha = 0.2)
}
} else {
tagCount <- getTagCount(tagMatrix , xlim = xlim, conf = conf, ...)
p <- ggplot(tagCount, aes(pos))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper),
linetype = 0, alpha = 0.2)
}
}
p <- p + geom_line(aes(y = value))
## x_scale for genebody
if(attr(tagMatrix, 'type') == 'body'){
## x_scale for gene body with no flank extension
if(is.null(upstream)){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(label[1],
"25%",
"50%",
"75%",
label[2]))
}
## x_scale for flank extension by relative value
if(inherits(upstream, 'rel')){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+25)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+50)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+75)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
nbin),
labels=c(paste0("-",as.numeric(upstream)*100,"%"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0("+",as.numeric(downstream)*100,"%")))
p <- p + geom_vline(xintercept=floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
linetype="longdash")
p <- p + geom_vline(xintercept=floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
linetype="longdash")
}
## x_scale for flank extension by absolute value
if(!is.null(upstream) & !inherits(upstream, 'rel')){
upstreamPer <- floor(upstream/1000)*0.1
downstreamPer <- floor(downstream/1000)*0.1
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.25)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.5)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.75)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
nbin),
labels=c(paste0("-",upstream,"bp"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0(downstream,"bp")))
p <- p + geom_vline(xintercept=floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
linetype="longdash")
p <- p + geom_vline(xintercept=floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
linetype="longdash")
}
}
## x_scale for start region
if(attr(tagMatrix, 'type') != 'body'){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(paste0("-",upstream,"bp"),
paste0("-",floor(upstream*0.5),"bp"),
label,
paste0(floor(downstream*0.5),"bp"),
paste0(downstream,"bp")))
p <- p + geom_vline(xintercept=floor(nbin*0.5),
linetype="longdash")
}
if (listFlag) {
cols <- getCols(length(tagMatrix))
p <- p + scale_color_manual(values=cols)
if (facet == "row") {
if (free_y) {
p <- p + facet_grid(.id ~ ., scales = "free_y")
} else {
p <- p + facet_grid(.id ~ .)
}
} else if (facet == "column") {
if (free_y) {
p <- p + facet_grid(. ~ .id, scales = "free_y")
} else {
p <- p + facet_grid(. ~ .id)
}
}
}
p <- p+xlab(xlab)+ylab(ylab)
p <- p + theme_bw() + theme(legend.title=element_blank())
if(facet != "none") {
p <- p + theme(legend.position="none")
}
return(p)
}
##' plot the profile of peaks automatically
##'
##' \code{peak} stands for the peak file.
##'
##' \code{by} the features of interest.
##'
##' (1) if users use \code{txdb}, \code{by} can be one of 'gene', 'transcript', 'exon',
##' 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.
##'
##' (2) if users use self-made granges object, \code{by} can be everything. Because this \code{by}
##' will not pass to functions to get features, which is different from the case of using
##' txdb object. This \code{by} is only used to made labels showed in picture.
##'
##' \code{type} means the property of the region. one of the "start site",
##' "end site" and "body".
##'
##' \code{upstream} and \code{downstream} parameter have different usages:
##'
##' (1) if \code{type == 'body'}, \code{upstream} and \code{downstream} can use to extend
##' the flank of body region.
##'
##' (2) if \code{type == 'start_site'/'end_site'}, \code{upstream} and \code{downstream} refer to
##' the upstream and downstream of the start_site or the end_site.
##'
##' \code{weightCol} refers to column in peak file. This column acts as a weight vaule. Details
##' see \url{https://github.com/YuLab-SMU/ChIPseeker/issues/15}
##'
##' \code{nbin} refers to the number of bins, providing a binning method
##' to get the tag matrix.
##'
##' \code{TxDb} parameter can accept txdb object.
##' But many regions can not be obtained by txdb object. In this case,
##' Users can provide self-made granges served the same role
##' as txdb object and pass to \code{TxDb} object.
##'
##' \code{plotPeakProf2()} is different from the \code{plotPeakProf()}. \code{plotPeakProf2()} do not
##' need to provide \code{window} parameter, which means \code{plotPeakProf2()} will call relevent
##' functions to make \code{window} automatically.
##'
##' @title plotPeakProf2
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object, or self-made granges object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param by e.g. 'gene', 'transcript', 'exon' or features of interest(e.g. "enhancer")
##' @param type one of "start_site", "end_site", "body"
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param verbose print message or not
##' @param nbin the amount of nbines
##' @param ignore_strand ignore the strand information or not
##' @param ... additional parameter
##' @return ggplot object
##' @export
##' @author G Yu, Ming Li
plotPeakProf2 <- function(peak,
upstream,
downstream,
conf,
by,
type,
weightCol = NULL,
TxDb = NULL,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet = "none",
free_y = TRUE,
verbose = TRUE,
nbin = NULL,
ignore_strand = FALSE,
...){
conf <- if(missingArg(conf)) NA else conf
upstream <- if(missingArg(upstream)) NULL else upstream
downstream <- if(missingArg(downstream)) NULL else downstream
if ( is(peak, "list") ) {
tagMatrix <- lapply(peak, getTagMatrix,
upstream = upstream,
downstream = downstream,
type = type,
TxDb = TxDb,
by = by,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand = ignore_strand)
} else {
tagMatrix <- getTagMatrix(peak = peak,
upstream = upstream,
downstream = downstream,
type = type,
by = by,
TxDb = TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand = ignore_strand)
}
if (!(missingArg(conf) || is.na(conf))){
p <- plotPeakProf(tagMatrix = tagMatrix,
conf = conf,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
...)
} else {
p <- plotPeakProf(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
facet= facet,
free_y = free_y,
...)
}
return(p)
}
##' plot the profile of peaks in two or more windows
##'
##'
##' This function comes from \url{https://github.com/YuLab-SMU/ChIPseeker/issues/189}
##'`
##' \code{plotPeakProf_MultiWindows()} is almost the same as \code{plotPeakProf2()}, having
##' the main difference of accepting two or more granges objects. Accepting more
##' granges objects can help compare the same peaks in different windows.
##'
##' \code{TxDb} parameter can accept txdb object.
##' But many regions can not be obtained by txdb object. In this case,
##' Users can provide self-made granges served the same role
##' as txdb object and pass to \code{TxDb} object.
##'
##' \code{by} the features of interest.
##'
##' (1) if users use \code{txdb}, \code{by} can be one of 'gene', 'transcript', 'exon',
##' 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.
##'
##' (2) if users use self-made granges object, \code{by} can be everything. Because this \code{by}
##' will not pass to functions to get features, which is different from the case of using
##' txdb object. This \code{by} is only used to made labels showed in picture.
##'
##' \code{type} means the property of the region. one of the "start site",
##' "end site" and "body".
##'
##' \code{upstream} and \code{downstream} parameter have different usages:
##'
##' (1) if \code{type == 'body'}, \code{upstream} and \code{downstream} can use to extend
##' the flank of body region.
##'
##' (2) if \code{type == 'start_site'/'end_site'}, \code{upstream} and \code{downstream} refer to
##' the upstream and downstream of the start_site or the end_site.
##'
##' \code{weightCol} refers to column in peak file. This column acts as a weight value. Details
##' see \url{https://github.com/YuLab-SMU/ChIPseeker/issues/15}
##'
##' \code{nbin} refers to the number of bins. \code{getTagMatrix()} provide a binning method
##' to get the tag matrix.
##'
##' There are two ways input a list of window.
##'
##' (1) Users can input a list of self-made granges objects
##'
##' (2) Users can input a list of \code{by} and only one \code{type}. In this way,
##' \code{plotPeakProf_MultiWindows()} can made a list of window from txdb object based on \code{by} and \code{type}.
##'
##' Warning:
##'
##' (1) All of these window should be the same type. It means users can only
##' compare a list of "start site"/"end site"/"body region" with the same upstream
##' and downstream.
##'
##' (2) So it will be only one \code{type} and several \code{by}.
##'
##' (3) Users can make window by txdb object or self-made granges object. Users can only
##' choose one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR' or 'UTR' in the
##' way of using txdb object. User can input any \code{by} in the way of using
##' self-made granges object.
##'
##' (4) Users can mingle the \code{by} designed for the two ways. \code{plotPeakProf_MultiWindows} can
##' accpet the hybrid \code{by}. But the above rules should be followed.
##'
##'
##' @title plotPeakProf_MultiWindows
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object or self-made granges objects
##' @param upstream upstream position
##' @param downstream downstream position
##' @param by feature of interest
##' @param type one of "start_site", "end_site", "body"
##' @param windows_name the name for each window, which will also be showed in the picture as labels
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param verbose print message or not
##' @param nbin the amount of bines
##' @param ignore_strand ignore the strand information or not
##' @param ... additional parameter
##' @return ggplot object
plotPeakProf_MultiWindows <- function(peak,
upstream,
downstream,
conf,
by,
type,
windows_name = NULL,
weightCol = NULL,
TxDb = NULL,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet = "row",
free_y = TRUE,
verbose = TRUE,
nbin = NULL,
ignore_strand = FALSE,
...){
conf <- if(missingArg(conf)) NA else conf
upstream <- if(missingArg(upstream)) NULL else upstream
downstream <- if(missingArg(downstream)) NULL else downstream
## check type
if(length(type) != 1){
stop("It should be only one type...")
}
## make the window name
if (is.null(windows_name)) {
nn <- by
warning("set the name automatically to ", paste(nn, collapse=' '))
windows_name <- nn
}else{
if (length(windows_name) != length(by)) {
stop("the length of the window name and the by should be equal...")
}
}
if ( is(peak, "list") ) {
tagMatrix <- lapply(peak, getTagMatrix2,
upstream=upstream,
downstream=downstream,
windows_name=windows_name,
type=type,
by=by,
TxDb=TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
} else {
tagMatrix <- getTagMatrix2(peak=peak,
upstream=upstream,
downstream=downstream,
windows_name=windows_name,
type=type,
by=by,
TxDb=TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
}
if (!(missingArg(conf) || is.na(conf))){
p <- plotMultiProf(tagMatrix = tagMatrix,
conf = conf,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
...)
} else {
p <- plotMultiProf(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
facet= facet,
free_y = free_y,
...)
}
return(p)
}
##' internal function for plotPeakProf_MultiWindows
##'
##' @param tagMatrix tagMatrix
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param ... additional parameter
plotMultiProf <- function(tagMatrix,
conf,
xlab="Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="none",
free_y = TRUE,
...){
if(is(tagMatrix[[1]][[1]],"matrix")){
upstream <- attr(tagMatrix[[1]][[1]], 'upstream')
downstream <- attr(tagMatrix[[1]][[1]], 'downstream')
# attr(tagMatrix, 'type') <- attr(tagMatrix[[1]][[1]], 'type')
# attr(tagMatrix, 'is.binning') <- attr(tagMatrix[[1]][[1]], 'is.binning')
binFlag <- attr(tagMatrix[[1]][[1]], 'is.binning')
type <- attr(tagMatrix[[1]][[1]], 'type')
}else{
upstream <- attr(tagMatrix[[1]], 'upstream')
downstream <- attr(tagMatrix[[1]], 'downstream')
binFlag <- attr(tagMatrix[[1]], 'is.binning')
type <- attr(tagMatrix[[1]], 'type')
}
if(type == "body"){
label <- c("SS","TS")
}else if(type == "start_site"){
label <- "SS"
}else{
label <- "TS"
}
if(binFlag){
if (!(missingArg(conf) || is.na(conf))){
plotMultiProf.binning(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
conf = conf,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}else{
plotMultiProf.binning(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}
}else{
xlim <- c(-upstream, downstream)
if (!(missingArg(conf) || is.na(conf))){
plotMultiProf.normal(tagMatrix = tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
conf = conf,
facet = facet,
free_y = free_y,
origin_label = label,
...)
}else{
plotMultiProf.normal(tagMatrix = tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = label,
...)
}
}
}
##' internal function
##'
##' @param tagMatrix tagMatrix
##' @param xlim xlim
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param origin_label the label of the center
##' @param verbose print message or not
##' @param ... additional parameter
plotMultiProf.normal <- function(tagMatrix, xlim,
xlab="Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet="none",
free_y = TRUE,
origin_label = "TSS",
verbose = TRUE,
...) {
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
if (verbose) {
cat(">> plotting figure...\t\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
conf <- if(missingArg(conf)) NA else conf
if (!(missingArg(conf) || is.na(conf))){
p <- plotMultiProf.normal.internal(tagMatrix = tagMatrix,
conf = conf,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = origin_label,
...)
} else {
p <- plotMultiProf.normal.internal(tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = origin_label,
...)
}
return(p)
}
##' internal function
##'
##'
##' @param tagMatrix tagMatrix
##' @param xlim xlim
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param origin_label the label of the center
##' @param ... additional parameter
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 geom_line
##' @importFrom ggplot2 geom_vline
##' @importFrom ggplot2 geom_ribbon
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 scale_color_manual
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 theme_bw
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 facet_grid
plotMultiProf.normal.internal <- function(tagMatrix, conf,
xlim = c(-3000,3000),
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="row",
free_y = TRUE,
origin_label,
...) {
listFlag <- FALSE
if (is.null(attr(tagMatrix[[1]],'upstream'))) {
if ( is.null(names(tagMatrix)) ) {
nn <- paste0("peak", seq_along(tagMatrix))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(tagMatrix) <- nn
## stop("tagMatrix should be a named list...")
}
listFlag <- TRUE
}
if ( listFlag ) {
facet <- match.arg(facet, c("none", "row", "column"))
if ( (xlim[2]-xlim[1]+1) != ncol(tagMatrix[[1]][[1]]) ) {
stop("please specify appropreate xcoordinations...")
}
} else {
if ( (xlim[2]-xlim[1]+1) != ncol(tagMatrix[[1]]) ) {
stop("please specify appropreate xcoordinations...")
}
}
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
##
conf <- if(missingArg(conf)) NA else conf
pos <- value <- .id <- Lower <- Upper <- NULL
if ( listFlag ) {
tagCount <- lapply(as.list(names(tagMatrix)), function(x){
tmp <- tagMatrix[[x]]
tagCount_tmp <- lapply(as.list(names(tmp)),function(x){
result <- getTagCount(tmp[[x]], xlim = xlim, conf = conf, ...)
result$type <- x
return(result)
})
tagCount_tmp <- list_to_dataframe(tagCount_tmp)
return(tagCount_tmp)
})
names(tagCount) <- names(tagMatrix)
tagCount <- list_to_dataframe(tagCount)
tagCount$.id <- factor(tagCount$.id, levels=names(tagMatrix))
p <- ggplot(tagCount, aes(pos, group=type, color=type))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = type),
linetype = 0, alpha = 0.2)
}
} else {
tagCount <- lapply(as.list(names(tagMatrix)), function(x){
result <- getTagCount(tagMatrix[[x]], xlim = xlim, conf = conf, ...)
result$type <- x
return(result)
})
tagCount <- do.call("rbind",tagCount)
p <- ggplot(tagCount, aes(x = pos))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper,fill = type),
linetype = 0, alpha = 0.2)
}
}
p <- p + geom_line(aes(y = value,color = type))
if ( 0 > xlim[1] && 0 < xlim[2] ) {
p <- p + geom_vline(xintercept=0,
linetype="longdash")
p <- p + scale_x_continuous(breaks=c(xlim[1], floor(xlim[1]/2),
0,
floor(xlim[2]/2), xlim[2]),
labels=c(paste0(xlim[1],"bp"), paste0(floor(xlim[1]/2),"bp"),
origin_label,
paste0(floor(xlim[2]/2),"bp"), paste0(xlim[2], "bp")))
}
if (listFlag) {
# cols <- getCols(length(tagMatrix[[1]]))
# p <- p + scale_color_manual(values=cols)
if (facet == "row") {
if (free_y) {
p <- p + facet_grid(.id ~ ., scales = "free_y")
} else {
p <- p + facet_grid(.id ~ .)
}
} else if (facet == "column") {
if (free_y) {
p <- p + facet_grid(. ~ .id, scales = "free_y")
} else {
p <- p + facet_grid(. ~ .id)
}
}
}
p <- p+xlab(xlab)+ylab(ylab)
p <- p + theme_bw() + theme(legend.title=element_blank())
# if(facet != "none") {
# p <- p + theme(legend.position="none")
# }
return(p)
}
##' internal function
##'
##' @param tagMatrix tagMatrix
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param upstream the upstream extension
##' @param downstream the downstream extension
##' @param label the label of the center
##' @param ... additional parameter
plotMultiProf.binning <- function(tagMatrix,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet ="none",
free_y = TRUE,
upstream = NULL,
downstream = NULL,
label,
...) {
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
conf <- if(missingArg(conf)) NA else conf
if (!(missingArg(conf) || is.na(conf))){
p <- plotMultiProf.binning.internal(tagMatrix ,
conf = conf,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
} else {
p <- plotMultiProf.binning.internal(tagMatrix ,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}
return(p)
}
##' internal function
##'
##' @param tagMatrix tagMatrix
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param upstream the upstream extension
##' @param downstream the downstream extension
##' @param label the label of the center
##' @param ... additional parameter
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 geom_line
##' @importFrom ggplot2 geom_vline
##' @importFrom ggplot2 geom_ribbon
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 scale_color_manual
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 theme_bw
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 facet_grid
##' @importFrom ggplot2 rel
plotMultiProf.binning.internal <- function(tagMatrix,
conf,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="none",
free_y = TRUE,
upstream = NULL,
downstream = NULL,
label,
...) {
listFlag <- FALSE
if (is(tagMatrix[[1]][[1]],"matrix")) {
if ( is.null(names(tagMatrix)) ) {
nn <- paste0("peak", seq_along(tagMatrix))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(tagMatrix) <- nn
## stop("tagMatrix should be a named list...")
}
listFlag <- TRUE
}
if(listFlag){
nbin <- dim(tagMatrix[[1]][[1]])[2]
type <- attr(tagMatrix[[1]][[1]], 'type')
}else{
nbin <- dim(tagMatrix[[1]])[2]
type <- attr(tagMatrix[[1]], 'type')
}
xlim <- c(1,nbin)
if ( listFlag ) {
facet <- match.arg(facet, c("none", "row", "column"))
}
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
##
conf <- if(missingArg(conf)) NA else conf
pos <- value <- .id <- Lower <- Upper <- NULL
if ( listFlag ) {
tagCount <- lapply(as.list(names(tagMatrix)), function(x){
tmp <- tagMatrix[[x]]
tagCount_tmp <- lapply(as.list(names(tmp)),function(x){
result <- getTagCount(tmp[[x]], xlim = xlim, conf = conf, ...)
result$type <- x
return(result)
})
tagCount_tmp <- list_to_dataframe(tagCount_tmp)
return(tagCount_tmp)
})
names(tagCount) <- names(tagMatrix)
tagCount <- list_to_dataframe(tagCount)
tagCount$.id <- factor(tagCount$.id, levels=names(tagMatrix))
p <- ggplot(tagCount, aes(pos, group=type, color=type))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = type),
linetype = 0, alpha = 0.2)
}
} else {
tagCount <- lapply(as.list(names(tagMatrix)), function(x){
result <- getTagCount(tagMatrix[[x]], xlim = xlim, conf = conf, ...)
result$type <- x
return(result)
})
tagCount <- do.call("rbind",tagCount)
p <- ggplot(tagCount, aes(pos,group=type,color=type))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper,fill = type),
linetype = 0, alpha = 0.2)
}
}
p <- p + geom_line(aes(y = value,color = type))
## x_scale for genebody
if(type == 'body'){
## x_scale for gene body with no flank extension
if(is.null(upstream)){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(label[1],
"25%",
"50%",
"75%",
label[2]))
}
## x_scale for flank extension by relative value
if(inherits(upstream, 'rel')){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+25)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+50)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+75)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
nbin),
labels=c(paste0("-",as.numeric(upstream)*100,"%"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0("+",as.numeric(downstream)*100,"%")))
p <- p + geom_vline(xintercept=floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
linetype="longdash")
p <- p + geom_vline(xintercept=floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
linetype="longdash")
}
## x_scale for flank extension by absolute value
if(!is.null(upstream) & !inherits(upstream, 'rel')){
upstreamPer <- floor(upstream/1000)*0.1
downstreamPer <- floor(downstream/1000)*0.1
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.25)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.5)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.75)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
nbin),
labels=c(paste0("-",upstream,"bp"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0(downstream,"bp")))
p <- p + geom_vline(xintercept=floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
linetype="longdash")
p <- p + geom_vline(xintercept=floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
linetype="longdash")
}
}
## x_scale for start region
if(type != 'body'){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(paste0("-",upstream,"bp"),
paste0("-",floor(upstream*0.5),"bp"),
label,
paste0(floor(downstream*0.5),"bp"),
paste0(downstream,"bp")))
p <- p + geom_vline(xintercept=floor(nbin*0.5),
linetype="longdash")
}
if (listFlag) {
if (facet == "row") {
if (free_y) {
p <- p + facet_grid(.id ~ ., scales = "free_y")
} else {
p <- p + facet_grid(.id ~ .)
}
} else if (facet == "column") {
if (free_y) {
p <- p + facet_grid(. ~ .id, scales = "free_y")
} else {
p <- p + facet_grid(. ~ .id)
}
}
}
p <- p+xlab(xlab)+ylab(ylab)
p <- p + theme_bw() + theme(legend.title=element_blank())
# if(facet != "none") {
# p <- p + theme(legend.position="none")
# }
return(p)
}
##' plot the heatmap of tagMatrix
##'
##'
##' @title tagHeatmap
##' @param tagMatrix tagMatrix or a list of tagMatrix
##' @param xlab xlab
##' @param ylab ylab
##' @param title title
##' @param palette palette to be filled in,details see \link[ggplot2]{scale_colour_brewer}
##' @param nrow the nrow of plotting a list of peak
##' @param ncol the ncol of plotting a list of peak
##' @return figure
##' @export
##' @author G Yu
tagHeatmap <- function(tagMatrix,
xlab="",
ylab="",
title=NULL,
palette="RdBu",
nrow = NULL,
ncol = NULL) {
listFlag <- FALSE
if (is(tagMatrix, "list")) {
listFlag <- TRUE
}
peakHeatmap.internal2(tagMatrix = tagMatrix,
listFlag = listFlag,
palette = palette,
xlab = xlab,
ylab = ylab,
title = title,
ncol = ncol,
nrow = nrow)
}
##' plot the heatmap of peaks
##'
##'
##' @title peakHeatmap
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param xlab xlab
##' @param ylab ylab
##' @param title title
##' @param palette palette to be filled in,details see \link[ggplot2]{scale_colour_brewer}
##' @param verbose print message or not
##' @param by one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'
##' @param type one of "start_site", "end_site", "body"
##' @param nbin the amount of nbines
##' @param ignore_strand ignore the strand information or not
##' @param windows a collection of region
##' @param nrow the nrow of plotting a list of peak
##' @param ncol the ncol of plotting a list of peak
##' @return figure
##' @export
##' @author G Yu
peakHeatmap <- function(peak, weightCol=NULL, TxDb=NULL,
upstream=1000, downstream=1000,
xlab="", ylab="", title=NULL,
palette=NULL, verbose=TRUE,
by="gene", type="start_site",
nbin = NULL,ignore_strand = FALSE,
windows,ncol = NULL, nrow = NULL) {
listFlag <- FALSE
if ( is(peak, "list") ) {
listFlag <- TRUE
if (is.null(names(peak)))
stop("peak should be a peak file or a name list of peak files...")
}
if (verbose) {
cat(">> preparing promoter regions...\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
if (verbose) {
cat(">> preparing tag matrix...\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
if(missing(windows)){
windows <- getBioRegion(TxDb=TxDb,
upstream=upstream,
downstream=downstream,
by=by,
type=type)
}
if (listFlag) {
tagMatrix <- lapply(peak, getTagMatrix,
weightCol=weightCol,
windows = windows,
upstream=upstream,
downstream=downstream,
TxDb = TxDb,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
names(tagMatrix) <- names(peak)
} else {
tagMatrix <- getTagMatrix(peak,
weightCol=weightCol,
windows = windows,
TxDb = TxDb,
upstream=upstream,
downstream=downstream,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
}
if (verbose) {
cat(">> generating figure...\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
xlim <- NULL
p <- peakHeatmap.internal2(tagMatrix = tagMatrix,
listFlag = listFlag,
palette = palette,
xlab = xlab,
ylab = ylab,
title = title,
nrow = nrow,
ncol = ncol)
if (verbose) {
cat(">> done...\t\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
invisible(tagMatrix)
p
}
##' @importFrom aplot plot_list
peakHeatmap.internal2 <- function(tagMatrix,
listFlag,
palette,
xlab,
ylab,
title,
nrow,
ncol) {
if ( is.null(xlab) || is.na(xlab))
xlab <- ""
if ( is.null(ylab) || is.na(ylab))
ylab <- ""
if (listFlag) {
nc <- length(tagMatrix)
if ( is.null(palette) || is.na(palette) ) {
palette <- getPalette(nc)
} else if (length(palette) != nc) {
palette <- rep(palette[1], nc)
} else {
palette <- palette
}
if (is.null(title) || is.na(title))
title <- names(tagMatrix)
if (length(xlab) != nc) {
xlab <- rep(xlab[1], nc)
}
if (length(ylab) != nc) {
ylab <- rep(ylab[1], nc)
}
if (length(title) != nc) {
title <- rep(title[1], nc)
}
tmp <- list()
for (i in 1:nc) {
p <- peakHeatmap.internal(tagMatrix = tagMatrix[[i]],
palette = palette[i],
xlab = xlab[i],
ylab = ylab[i],
title= title[i])
p <- p + theme(plot.title = element_text(hjust = 0.5))
tmp[[i]] <- p
}
if(is.null(nrow) && is.null(ncol))
nrow <- 1
p <- plot_list(gglist = tmp,
ncol = ncol,
nrow = nrow)
return(p)
} else {
if (is.null(palette) || is.na(palette))
palette <- "RdBu"
if (is.null(title) || is.na(title))
title <- ""
peakHeatmap.internal(tagMatrix = tagMatrix,
palette = palette,
xlab = xlab,
ylab = ylab,
title = title)
}
}
##' @import BiocGenerics
##' @importFrom yulab.utils mat2df
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 aes
##' @importFrom ggplot2 geom_tile
##' @importFrom ggplot2 scale_fill_distiller
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 labs
##' @importFrom ggplot2 scale_x_continuous
peakHeatmap.internal <- function(tagMatrix,
palette="RdBu",
xlab="",
ylab="",
title="") {
upstream <- attr(tagMatrix, "upstream")
downstream <- attr(tagMatrix, "downstream")
binning_Flag <- attr(tagMatrix,"is.binning")
type <- attr(tagMatrix,"type")
body_Flag <- FALSE
if(type == "body"){
body_Flag <- TRUE
label <- attr(tagMatrix,"label")
}
if(binning_Flag){
nbin <- dim(tagMatrix)[2]
}
tagMatrix <- t(apply(tagMatrix, 1, function(x) x/max(x)))
ii <- order(rowSums(tagMatrix))
tagMatrix <- tagMatrix[ii,]
colnames(tagMatrix) <- seq_len(dim(tagMatrix)[2])
rownames(tagMatrix) <- seq_len(dim(tagMatrix)[1])
tagMatrix <- mat2df(tagMatrix)
colnames(tagMatrix) <- c("values","sample_ID","coordinate")
sample_ID <- coordinate <- NULL
p <- ggplot(tagMatrix, aes(x = coordinate,y = sample_ID)) +
geom_tile(aes(fill = values)) +
scale_fill_distiller(palette = palette) +
theme(axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.line.y = element_blank(),
panel.grid=element_blank(),
panel.background = element_blank()) +
labs(x = xlab, y = ylab, title = title)
if(body_Flag){
if(inherits(upstream, 'rel')){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+25)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+50)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+75)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
nbin),
labels=c(paste0("-",as.numeric(upstream)*100,"%"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0("+",as.numeric(downstream)*100,"%")))
}
if(is.null(upstream)){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(label[1],
"25%",
"50%",
"75%",
label[2]))
}
if(!is.null(upstream) && !inherits(upstream, 'rel')){
upstreamPer <- floor(upstream/1000)*0.1
downstreamPer <- floor(downstream/1000)*0.1
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.25)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.5)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.75)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
nbin),
labels=c(paste0("-",upstream,"bp"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0(downstream,"bp")))
}
p <- p + scale_y_continuous(expand = c(0,0))
return(p)
}
if(binning_Flag){
p <- p + scale_x_continuous(breaks = c(1,
floor(nbin*(downstream*0.5/(downstream+upstream))),
floor(nbin*(downstream/(downstream+upstream))),
floor(nbin*((downstream + upstream*0.5)/(downstream+upstream))),
nbin),
labels = c((-1*downstream),
floor(-1*downstream*0.5),
0,
floor(upstream*0.5),
upstream))
}else{
p <- p + scale_x_continuous(labels = function(x) x - upstream)
}
p <- p + scale_y_continuous(expand = c(0,0))
p
}
##' plot the heatmap of peaks align to a sets of regions
##'
##'
##' @title peakHeatmap
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param xlab xlab
##' @param ylab ylab
##' @param title title
##' @param palette palette to be filled in,details see \link[ggplot2]{scale_colour_brewer}
##' @param verbose print message or not
##' @param by one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'
##' @param type one of "start_site", "end_site", "body"
##' @param nbin the amount of nbines
##' @param ignore_strand ignore the strand information or not
##' @param windows_name the name for each window, which will also be showed in the picture as labels
##' @param nrow the nrow of plotting a list of peak
##' @param ncol the ncol of plotting a list of peak
##' @param facet_label_text_size the size of facet label text
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 aes
##' @importFrom ggplot2 geom_tile
##' @importFrom ggplot2 scale_fill_distiller
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 labs
##' @importFrom ggplot2 scale_x_continuous
##' @return figure
##' @export
peakHeatmap_multiple_Sets <- function(peak,
weightCol=NULL,
TxDb=NULL,
upstream=1000,
downstream=1000,
xlab="",
ylab="",
title=NULL,
palette=NULL,
verbose=TRUE,
by="gene",
type="start_site",
nbin = NULL,
ignore_strand = FALSE,
windows_name = NULL,
ncol = NULL,
nrow = NULL,
facet_label_text_size = 12){
listFlag <- FALSE
if ( is(peak, "list") ) {
listFlag <- TRUE
if (is.null(names(peak)))
stop("peak should be a peak file or a name list of peak files...")
}
if (verbose) {
cat(">> preparing promoter regions...\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
## check type
if(length(type) != 1){
stop("It should be only one type...")
}
if(is.null(windows_name) && !is.null(names(TxDb)))
windows_name <- names(TxDb)
## make the window name
if (is.null(windows_name)) {
nn <- by
warning("set the name automatically to ", paste(nn, collapse=' '))
windows_name <- nn
}else{
if (length(windows_name) != length(by)) {
stop("the length of the window name and the by should be equal...")
}
}
if ( is(peak, "list") ) {
tagMatrix <- lapply(peak, getTagMatrix2,
upstream=upstream,
downstream=downstream,
windows_name=windows_name,
type=type,
by=by,
TxDb=TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
} else {
tagMatrix <- getTagMatrix2(peak=peak,
upstream=upstream,
downstream=downstream,
windows_name=windows_name,
type=type,
by=by,
TxDb=TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
}
if(listFlag){
nc <- length(tagMatrix)
if ( is.null(palette) || is.na(palette) ) {
palette <- getPalette(nc)
} else if (length(palette) != nc) {
palette <- rep(palette[1], nc)
} else {
palette <- palette
}
if (is.null(title) || is.na(title))
title <- names(tagMatrix)
if (length(xlab) != nc) {
xlab <- rep(xlab[1], nc)
}
if (length(ylab) != nc) {
ylab <- rep(ylab[1], nc)
}
if (length(title) != nc) {
title <- rep(title[1], nc)
}
tmp <- list()
for (i in 1:nc) {
p <- peakHeatmap_multiple_Sets.internal(tagMatrix = tagMatrix[[i]],
upstream=upstream,
downstream=downstream,
xlab=xlab[[i]],
ylab=ylab[[i]],
title=title[[i]],
palette=palette[[i]],
ncol = ncol,
nrow = nrow,
facet_label_text_size = facet_label_text_size)
p <- p + theme(plot.title = element_text(hjust = 0.5))
tmp[[i]] <- p
}
if(is.null(nrow) && is.null(ncol))
nrow <- 1
p <- plot_list(gglist = tmp,
ncol = ncol,
nrow = nrow)
}else{
if (is.null(palette) || is.na(palette))
palette <- "RdBu"
if (is.null(title) || is.na(title))
title <- ""
p <- peakHeatmap_multiple_Sets.internal(tagMatrix = tagMatrix,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette,
ncol = ncol,
nrow = nrow,
facet_label_text_size = facet_label_text_size)
}
return(p)
}
##' @importFrom yulab.utils mat2df
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 aes
##' @importFrom ggplot2 geom_tile
##' @importFrom ggplot2 scale_fill_distiller
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 labs
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 facet_grid
##' @importFrom ggplot2 element_text
##' @importFrom ggplot2 element_blank
peakHeatmap_multiple_Sets.internal <- function(tagMatrix,
upstream=1000,
downstream=1000,
xlab="",
ylab="",
title=NULL,
palette=NULL,
ncol = NULL,
nrow = NULL,
facet_label_text_size = 12){
binning_Flag <- attr(tagMatrix[[1]],"is.binning")
if(binning_Flag) nbin <- dim(tagMatrix[[1]])[2]
type <- attr(tagMatrix,"type")
body_Flag <- FALSE
if(attr(tagMatrix[[1]],"type") == "body"){
body_Flag <- TRUE
label <- attr(tagMatrix,"label")
}
name_of_list <- as.list(names(tagMatrix))
peak_list <- lapply(name_of_list,function(x){
tagMatrix[[x]] <- t(apply(tagMatrix[[x]], 1, function(x) x/max(x)))
ii <- order(rowSums(tagMatrix[[x]]))
tagMatrix[[x]] <- tagMatrix[[x]][ii,]
colnames(tagMatrix[[x]]) <- seq_len(dim(tagMatrix[[x]])[2])
rownames(tagMatrix[[x]]) <- seq_len(dim(tagMatrix[[x]])[1])
tagMatrix[[x]] <- mat2df(tagMatrix[[x]])
colnames(tagMatrix[[x]]) <- c("values","sample_ID","coordinate")
tagMatrix[[x]]$sample <- x
return(tagMatrix[[x]])
})
peak_df <- list_to_dataframe(peak_list)
sample_ID <- coordinate <- NULL
p <- ggplot(peak_df, aes(x = coordinate,y = sample_ID)) +
geom_tile(aes(fill = values)) +
scale_fill_distiller(palette = palette) +
theme(axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.line.y = element_blank(),
panel.grid=element_blank(),
panel.background = element_blank()) +
labs(x = xlab, y = ylab, title = title)
if(body_Flag){
if(inherits(upstream, 'rel')){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+25)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+50)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+75)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
nbin),
labels=c(paste0("-",as.numeric(upstream)*100,"%"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0("+",as.numeric(downstream)*100,"%")))
}
if(is.null(upstream)){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(label[1],
"25%",
"50%",
"75%",
label[2]))
}
if(!is.null(upstream) && !inherits(upstream, 'rel')){
upstreamPer <- floor(upstream/1000)*0.1
downstreamPer <- floor(downstream/1000)*0.1
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.25)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.5)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.75)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
nbin),
labels=c(paste0("-",upstream,"bp"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0(downstream,"bp")))
}
p <- p + facet_grid(sample ~ .,switch = "y",space = "free_y",scales = "free_y") +
theme(strip.text.y.left = element_text(color = "black",face = "bold",
size = facet_label_text_size),
strip.background = element_blank())
return(p)
}
if(binning_Flag){
p <- p + scale_x_continuous(breaks = c(1,
floor(nbin*(downstream*0.5/(downstream+upstream))),
floor(nbin*(downstream/(downstream+upstream))),
floor(nbin*((downstream + upstream*0.5)/(downstream+upstream))),
nbin),
labels = c((-1*downstream),
floor(-1*downstream*0.5),
0,
floor(upstream*0.5),
upstream))
}else{
p <- p + scale_x_continuous(breaks = c(1,
floor(downstream*0.5),
(downstream + 1),
(downstream + 1 + floor(upstream * 0.5)),
upstream+downstream+1),
labels = c((-1*downstream),
floor(-1*downstream*0.5),
0,
floor(upstream*0.5),
upstream))
}
p <- p + facet_grid(sample ~ .,switch = "y",scales = "free_y",space = "free") +
theme(strip.text.y.left = element_text(color = "black",face = "bold",
size = facet_label_text_size),
strip.background = element_blank()) +
scale_y_continuous(expand = c(0,0))
return(p)
}
##' plot peak heatmap and profile in a picture
##'
##'
##' @title peak_Profile_Heatmap
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param xlab xlab
##' @param ylab ylab
##' @param title title
##' @param palette palette to be filled in,details see \link[ggplot2]{scale_colour_brewer}
##' @param verbose print message or not
##' @param by one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'
##' @param type one of "start_site", "end_site", "body"
##' @param nbin the amount of nbines
##' @param ignore_strand ignore the strand information or not
##' @param windows_name the name for each window, which will also be showed in the picture as labels
##' @param nrow the nrow of plotting a list of peak
##' @param ncol the ncol of plotting a list of peak
##' @param facet_label_text_size the size of facet label text
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param height_proportion the proportion of profiling picture and heatmap
##' @importFrom aplot insert_bottom
##' @importFrom aplot plot_list
##' @export
peak_Profile_Heatmap <- function(peak,
weightCol=NULL,
TxDb=NULL,
upstream=1000,
downstream=1000,
xlab="",
ylab="",
title=NULL,
palette=NULL,
verbose=TRUE,
by="gene",
type="start_site",
nbin = NULL,
ignore_strand = FALSE,
windows_name = NULL,
ncol = NULL,
nrow = NULL,
facet_label_text_size = 12,
conf,
facet = "row",
free_y = TRUE,
height_proportion = 4){
conf <- if(missingArg(conf)) NA else conf
if(is(peak, "list")){
nc <- length(peak)
tmp <- list()
if ( is.null(names(peak)) ) {
nn <- paste0("peak", seq_along(peak))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(peak) <- nn
## stop("tagMatrix should be a named list...")
}
if(is.null(palette)) palette <- getPalette(nc)
if(is.null(title)) title_of_plot <- names(peak)
for (i in 1:nc) {
peak_profile <- plotPeakProf(peak = peak[[i]],
upstream = upstream,
downstream = downstream,
conf = conf,
by = by,
type = type,
windows_name = windows_name,
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
nbin = nbin,
ignore_strand = ignore_strand)
peak_profile <- peak_profile + labs(title = title_of_plot[i]) +
theme(plot.title = element_text(hjust = 0.5))
if(length(by) != 1){
peak_heatmap <- peakHeatmap_multiple_Sets(peak = peak[[i]],
weightCol=weightCol,
TxDb=TxDb,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette[[i]],
verbose=verbose,
by=by,
type=type,
nbin = nbin,
ignore_strand = ignore_strand,
windows_name = windows_name,
ncol = ncol,
nrow = nrow,
facet_label_text_size = facet_label_text_size)
}else{
peak_heatmap <- peakHeatmap(peak[[i]],
weightCol=weightCol,
TxDb=TxDb,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette[[i]],
verbose=verbose,
by=by,
type=type,
nbin = nbin,
ignore_strand = ignore_strand,
ncol = ncol,
nrow = nrow)
}
p <- peak_profile %>%
insert_bottom(peak_heatmap,height = height_proportion)
tmp[[i]] <- p
}
if (is.null(ncol) && is.null(nrow))
nrow <- 1
p <- plot_list(gglist = tmp,
ncol = ncol,
nrow = nrow)
return(p)
}
peak_profile <- plotPeakProf(peak = peak,
upstream = upstream,
downstream = downstream,
conf = conf,
by = by,
type = type,
windows_name = windows_name,
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
nbin = nbin,
ignore_strand = ignore_strand)
if(length(by) != 1){
peak_heatmap <- peakHeatmap_multiple_Sets(peak = peak,
weightCol=weightCol,
TxDb=TxDb,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette,
verbose=verbose,
by=by,
type=type,
nbin = nbin,
ignore_strand = ignore_strand,
windows_name = windows_name,
ncol = ncol,
nrow = nrow,
facet_label_text_size = facet_label_text_size)
}else{
peak_heatmap <- peakHeatmap(peak = peak,
weightCol=weightCol,
TxDb=TxDb,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette,
verbose=verbose,
by=by,
type=type,
nbin = nbin,
ignore_strand = ignore_strand,
ncol = ncol,
nrow = nrow)
}
p <- peak_profile %>%
insert_bottom(peak_heatmap,height = height_proportion)
return(p)
}
YuLab-SMU/ChIPseeker documentation built on Nov. 2, 2024, 1:45 p.m.
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Defines functions plotAvgProf.internal plotAvgProf plotPeakProf
Documented in plotAvgProf plotPeakProf
##' plot the profile of peaks
##'`
##' \code{plotPeakProf_MultiWindows()} is almost the same as \code{plotPeakProf2()}, having
##' the main difference of accepting two or more granges objects. Accepting more
##' granges objects can help compare the same peaks in different windows.
##'
##' \code{TxDb} parameter can accept txdb object.
##' But many regions can not be obtained by txdb object. In this case,
##' Users can provide self-made granges served the same role
##' as txdb object and pass to \code{TxDb} object.
##'
##' \code{by} the features of interest.
##'
##' (1) if users use \code{txdb}, \code{by} can be one of 'gene', 'transcript', 'exon',
##' 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.
##'
##' (2) if users use self-made granges object, \code{by} can be everything. Because this \code{by}
##' will not pass to functions to get features, which is different from the case of using
##' txdb object. This \code{by} is only used to made labels showed in picture.
##'
##' \code{type} means the property of the region. one of the "start site",
##' "end site" and "body".
##'
##' \code{upstream} and \code{downstream} parameter have different usages:
##'
##' (1) if \code{type == 'body'}, \code{upstream} and \code{downstream} can use to extend
##' the flank of body region.
##'
##' (2) if \code{type == 'start_site'/'end_site'}, \code{upstream} and \code{downstream} refer to
##' the upstream and downstream of the start_site or the end_site.
##'
##' \code{weightCol} refers to column in peak file. This column acts as a weight value. Details
##' see \url{https://github.com/YuLab-SMU/ChIPseeker/issues/15}
##'
##' \code{nbin} refers to the number of bins. \code{getTagMatrix()} provide a binning method
##' to get the tag matrix.
##'
##' There are two ways input a list of window.
##'
##' (1) Users can input a list of self-made granges objects
##'
##' (2) Users can input a list of \code{by} and only one \code{type}. In this way,
##' \code{plotPeakProf_MultiWindows()} can made a list of window from txdb object based on \code{by} and \code{type}.
##'
##' Warning:
##'
##' (1) All of these window should be the same type. It means users can only
##' compare a list of "start site"/"end site"/"body region" with the same upstream
##' and downstream.
##'
##' (2) So it will be only one \code{type} and several \code{by}.
##'
##' (3) Users can make window by txdb object or self-made granges object. Users can only
##' choose one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR' or 'UTR' in the
##' way of using txdb object. User can input any \code{by} in the way of using
##' self-made granges object.
##'
##' (4) Users can mingle the \code{by} designed for the two ways. \code{plotPeakProf_MultiWindows} can
##' accpet the hybrid \code{by}. But the above rules should be followed.
##'
##' \url{https://github.com/YuLab-SMU/ChIPseeker/issues/189}
##'
##' @title plotPeakProf_MultiWindows
##'
##' @param tagMatrix tagMatrix or a list of tagMatrix
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object or self-made granges objects
##' @param upstream upstream position
##' @param downstream downstream position
##' @param by feature of interest
##' @param type one of "start_site", "end_site", "body"
##' @param windows_name the name for each window, which will also be showed in the picture as labels
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param verbose print message or not
##' @param nbin the amount of bines
##' @param ignore_strand ignore the strand information or not
##' @param ... additional parameter
##' @return ggplot object
##' @importFrom methods is
##' @importFrom methods as
##' @importFrom methods missingArg
##' @importFrom methods new
##' @export
plotPeakProf <- function(tagMatrix = NULL,
peak,
upstream,
downstream,
conf,
by,
type,
windows_name = NULL,
weightCol = NULL,
TxDb = NULL,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet = "row",
free_y = TRUE,
verbose = TRUE,
nbin = NULL,
ignore_strand = FALSE,
...){
if(is.null(tagMatrix)){
conf <- if(missingArg(conf)) NA else conf
upstream <- if(missingArg(upstream)) NULL else upstream
downstream <- if(missingArg(downstream)) NULL else downstream
if(length(by) == 1){
plotPeakProf2(peak = peak,
upstream = upstream,
downstream = downstream,
conf = conf,
by = by,
type = type,
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
nbin = nbin,
ignore_strand = ignore_strand,
...)
}else{
if(is.null(windows_name) && !is.null(names(TxDb)))
windows_name <- names(TxDb)
plotPeakProf_MultiWindows(peak = peak,
upstream = upstream,
downstream = downstream,
conf = conf,
by = by,
type = type,
windows_name = windows_name,
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
nbin = nbin,
ignore_strand = ignore_strand,
...)
}
}else{
if(is(tagMatrix, "list")){
upstream <- attr(tagMatrix[[1]], 'upstream')
downstream <- attr(tagMatrix[[1]], 'downstream')
label <- attr(tagMatrix[[1]], 'label')
attr(tagMatrix, 'type') <- attr(tagMatrix[[1]], 'type')
attr(tagMatrix, 'is.binning') <- attr(tagMatrix[[1]], 'is.binning')
}else{
upstream <- attr(tagMatrix, 'upstream')
downstream <- attr(tagMatrix, 'downstream')
label <- attr(tagMatrix, 'label')
}
if(attr(tagMatrix, 'is.binning')){
if (!(missingArg(conf) || is.na(conf))){
plotAvgProf.binning(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
conf = conf,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}else{
plotAvgProf.binning(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}
}else{
xlim <- c(-upstream, downstream)
if (!(missingArg(conf) || is.na(conf))){
plotAvgProf (tagMatrix = tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
conf = conf,
facet = facet,
free_y = free_y,
origin_label = label,
...)
}else{
plotAvgProf (tagMatrix = tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = label,
...)
}
}
}
}
##' plot the profile of peaks
##'
##'
##' @title plotAvgProf
##' @param tagMatrix tagMatrix or a list of tagMatrix
##' @param xlim xlim
##' @param xlab x label
##' @param ylab y label
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param origin_label label of the center
##' @param verbose print message or not
##' @param ... additional parameter
##' @return ggplot object
##' @author G Yu; Y Yan
##' @export
plotAvgProf <- function(tagMatrix, xlim,
xlab="Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet="none",
free_y = TRUE,
origin_label = "TSS",
verbose = TRUE,
...) {
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
if (verbose) {
cat(">> plotting figure...\t\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
conf <- if(missingArg(conf)) NA else conf
if (!(missingArg(conf) || is.na(conf))){
p <- plotAvgProf.internal(tagMatrix = tagMatrix,
conf = conf,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = origin_label,
...)
} else {
p <- plotAvgProf.internal(tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = origin_label,
...)
}
return(p)
}
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 geom_line
##' @importFrom ggplot2 geom_vline
##' @importFrom ggplot2 geom_ribbon
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 scale_color_manual
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 theme_bw
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 facet_grid
plotAvgProf.internal <- function(tagMatrix, conf,
xlim = c(-3000,3000),
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="none",
free_y = TRUE,
origin_label,
...) {
listFlag <- FALSE
if (is(tagMatrix, "list")) {
if ( is.null(names(tagMatrix)) ) {
nn <- paste0("peak", seq_along(tagMatrix))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(tagMatrix) <- nn
## stop("tagMatrix should be a named list...")
}
listFlag <- TRUE
}
if ( listFlag ) {
facet <- match.arg(facet, c("none", "row", "column"))
if ( (xlim[2]-xlim[1]+1) != ncol(tagMatrix[[1]]) ) {
stop("please specify appropreate xcoordinations...")
}
} else {
if ( (xlim[2]-xlim[1]+1) != ncol(tagMatrix) ) {
stop("please specify appropreate xcoordinations...")
}
}
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
##
conf <- if(missingArg(conf)) NA else conf
pos <- value <- .id <- Lower <- Upper <- NULL
if ( listFlag ) {
tagCount <- lapply(tagMatrix, function(x) getTagCount(x, xlim = xlim, conf = conf, ...))
tagCount <- list_to_dataframe(tagCount)
tagCount$.id <- factor(tagCount$.id, levels=names(tagMatrix))
p <- ggplot(tagCount, aes(pos, group=.id, color=.id))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = .id),
linetype = 0, alpha = 0.2)
}
} else {
tagCount <- getTagCount(tagMatrix, xlim = xlim, conf = conf, ...)
p <- ggplot(tagCount, aes(pos))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper),
linetype = 0, alpha = 0.2)
}
}
p <- p + geom_line(aes(y = value))
if ( 0 > xlim[1] && 0 < xlim[2] ) {
p <- p + geom_vline(xintercept=0,
linetype="longdash")
p <- p + scale_x_continuous(breaks=c(xlim[1], floor(xlim[1]/2),
0,
floor(xlim[2]/2), xlim[2]),
labels=c(paste0(xlim[1],"bp"), paste0(floor(xlim[1]/2),"bp"),
origin_label,
paste0(floor(xlim[2]/2),"bp"), paste0(xlim[2], "bp")))
}
if (listFlag) {
cols <- getCols(length(tagMatrix))
p <- p + scale_color_manual(values=cols)
if (facet == "row") {
if (free_y) {
p <- p + facet_grid(.id ~ ., scales = "free_y")
} else {
p <- p + facet_grid(.id ~ .)
}
} else if (facet == "column") {
if (free_y) {
p <- p + facet_grid(. ~ .id, scales = "free_y")
} else {
p <- p + facet_grid(. ~ .id)
}
}
}
p <- p+xlab(xlab)+ylab(ylab)
p <- p + theme_bw() + theme(legend.title=element_blank())
if(facet != "none") {
p <- p + theme(legend.position="none")
}
return(p)
}
##' plot the profile of peaks that align to flank sequences of TSS
##'
##' This function is the old function of \code{plotPeakProf2}. It can
##' only plot the start site region of gene.
##'
##' @title plotAvgProf
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param verbose print message or not
##' @param ignore_strand ignore the strand information or not
##' @param ... additional parameter
##' @return ggplot object
##' @export
##' @author G Yu, Ming L
plotAvgProf2 <- function(peak, weightCol = NULL, TxDb = NULL,
upstream = 1000, downstream = 1000,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet = "none",
free_y = TRUE,
verbose = TRUE,
ignore_strand = FALSE,
...) {
plotPeakProf2(peak = peak,
upstream = upstream,
downstream = downstream,
conf,
by = "gene",
type = "start_site",
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
ignore_strand = ignore_strand,
...)
}
##' plot the profile of peaks by binning
##'
##'
##' @title plotAvgProf.binning
##' @param tagMatrix tagMatrix or a list of tagMatrix
##' @param xlab x label
##' @param ylab y label
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled
##' @param upstream rel object reflects the percentage of flank extension, e.g rel(0.2)
##' integer reflects the actual length of flank extension or TSS region
##' NULL reflects the gene body with no extension
##' @param downstream rel object reflects the percentage of flank extension, e.g rel(0.2)
##' integer reflects the actual length of flank extension or TSS region
##' NULL reflects the gene body with no extension
##' @param label label
##' @param ... additional parameter
##' @return ggplot object
##' @importFrom ggplot2 rel
plotAvgProf.binning <- function(tagMatrix,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet ="none",
free_y = TRUE,
upstream = NULL,
downstream = NULL,
label,
...) {
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
conf <- if(missingArg(conf)) NA else conf
if (!(missingArg(conf) || is.na(conf))){
p <- plotAvgProf.binning.internal(tagMatrix ,
conf = conf,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
} else {
p <- plotAvgProf.binning.internal(tagMatrix ,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}
return(p)
}
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 geom_line
##' @importFrom ggplot2 geom_vline
##' @importFrom ggplot2 geom_ribbon
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 scale_color_manual
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 theme_bw
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 facet_grid
##' @importFrom ggplot2 rel
plotAvgProf.binning.internal <- function(tagMatrix,
conf,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="none",
free_y = TRUE,
upstream = NULL,
downstream = NULL,
label,
...) {
listFlag <- FALSE
if (is(tagMatrix, "list")) {
if ( is.null(names(tagMatrix )) ) {
nn <- paste0("peak", seq_along(tagMatrix ))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(tagMatrix) <- nn
## stop("tagMatrix should be a named list...")
}
listFlag <- TRUE
}
if(listFlag){
nbin <- dim(tagMatrix[[1]])[2]
}else{
nbin <- dim(tagMatrix)[2]
}
xlim <- c(1,nbin)
if ( listFlag ) {
facet <- match.arg(facet, c("none", "row", "column"))
}
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
##
conf <- if(missingArg(conf)) NA else conf
pos <- value <- .id <- Lower <- Upper <- NULL
if ( listFlag ) {
tagCount <- lapply(tagMatrix , function(x) getTagCount(x, xlim = xlim, conf = conf, ...))
tagCount <- list_to_dataframe(tagCount)
tagCount$.id <- factor(tagCount$.id, levels=names(tagMatrix ))
p <- ggplot(tagCount, aes(pos, group=.id, color=.id))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = .id),
linetype = 0, alpha = 0.2)
}
} else {
tagCount <- getTagCount(tagMatrix , xlim = xlim, conf = conf, ...)
p <- ggplot(tagCount, aes(pos))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper),
linetype = 0, alpha = 0.2)
}
}
p <- p + geom_line(aes(y = value))
## x_scale for genebody
if(attr(tagMatrix, 'type') == 'body'){
## x_scale for gene body with no flank extension
if(is.null(upstream)){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(label[1],
"25%",
"50%",
"75%",
label[2]))
}
## x_scale for flank extension by relative value
if(inherits(upstream, 'rel')){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+25)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+50)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+75)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
nbin),
labels=c(paste0("-",as.numeric(upstream)*100,"%"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0("+",as.numeric(downstream)*100,"%")))
p <- p + geom_vline(xintercept=floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
linetype="longdash")
p <- p + geom_vline(xintercept=floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
linetype="longdash")
}
## x_scale for flank extension by absolute value
if(!is.null(upstream) & !inherits(upstream, 'rel')){
upstreamPer <- floor(upstream/1000)*0.1
downstreamPer <- floor(downstream/1000)*0.1
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.25)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.5)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.75)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
nbin),
labels=c(paste0("-",upstream,"bp"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0(downstream,"bp")))
p <- p + geom_vline(xintercept=floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
linetype="longdash")
p <- p + geom_vline(xintercept=floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
linetype="longdash")
}
}
## x_scale for start region
if(attr(tagMatrix, 'type') != 'body'){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(paste0("-",upstream,"bp"),
paste0("-",floor(upstream*0.5),"bp"),
label,
paste0(floor(downstream*0.5),"bp"),
paste0(downstream,"bp")))
p <- p + geom_vline(xintercept=floor(nbin*0.5),
linetype="longdash")
}
if (listFlag) {
cols <- getCols(length(tagMatrix))
p <- p + scale_color_manual(values=cols)
if (facet == "row") {
if (free_y) {
p <- p + facet_grid(.id ~ ., scales = "free_y")
} else {
p <- p + facet_grid(.id ~ .)
}
} else if (facet == "column") {
if (free_y) {
p <- p + facet_grid(. ~ .id, scales = "free_y")
} else {
p <- p + facet_grid(. ~ .id)
}
}
}
p <- p+xlab(xlab)+ylab(ylab)
p <- p + theme_bw() + theme(legend.title=element_blank())
if(facet != "none") {
p <- p + theme(legend.position="none")
}
return(p)
}
##' plot the profile of peaks automatically
##'
##' \code{peak} stands for the peak file.
##'
##' \code{by} the features of interest.
##'
##' (1) if users use \code{txdb}, \code{by} can be one of 'gene', 'transcript', 'exon',
##' 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.
##'
##' (2) if users use self-made granges object, \code{by} can be everything. Because this \code{by}
##' will not pass to functions to get features, which is different from the case of using
##' txdb object. This \code{by} is only used to made labels showed in picture.
##'
##' \code{type} means the property of the region. one of the "start site",
##' "end site" and "body".
##'
##' \code{upstream} and \code{downstream} parameter have different usages:
##'
##' (1) if \code{type == 'body'}, \code{upstream} and \code{downstream} can use to extend
##' the flank of body region.
##'
##' (2) if \code{type == 'start_site'/'end_site'}, \code{upstream} and \code{downstream} refer to
##' the upstream and downstream of the start_site or the end_site.
##'
##' \code{weightCol} refers to column in peak file. This column acts as a weight vaule. Details
##' see \url{https://github.com/YuLab-SMU/ChIPseeker/issues/15}
##'
##' \code{nbin} refers to the number of bins, providing a binning method
##' to get the tag matrix.
##'
##' \code{TxDb} parameter can accept txdb object.
##' But many regions can not be obtained by txdb object. In this case,
##' Users can provide self-made granges served the same role
##' as txdb object and pass to \code{TxDb} object.
##'
##' \code{plotPeakProf2()} is different from the \code{plotPeakProf()}. \code{plotPeakProf2()} do not
##' need to provide \code{window} parameter, which means \code{plotPeakProf2()} will call relevent
##' functions to make \code{window} automatically.
##'
##' @title plotPeakProf2
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object, or self-made granges object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param by e.g. 'gene', 'transcript', 'exon' or features of interest(e.g. "enhancer")
##' @param type one of "start_site", "end_site", "body"
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param verbose print message or not
##' @param nbin the amount of nbines
##' @param ignore_strand ignore the strand information or not
##' @param ... additional parameter
##' @return ggplot object
##' @export
##' @author G Yu, Ming Li
plotPeakProf2 <- function(peak,
upstream,
downstream,
conf,
by,
type,
weightCol = NULL,
TxDb = NULL,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet = "none",
free_y = TRUE,
verbose = TRUE,
nbin = NULL,
ignore_strand = FALSE,
...){
conf <- if(missingArg(conf)) NA else conf
upstream <- if(missingArg(upstream)) NULL else upstream
downstream <- if(missingArg(downstream)) NULL else downstream
if ( is(peak, "list") ) {
tagMatrix <- lapply(peak, getTagMatrix,
upstream = upstream,
downstream = downstream,
type = type,
TxDb = TxDb,
by = by,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand = ignore_strand)
} else {
tagMatrix <- getTagMatrix(peak = peak,
upstream = upstream,
downstream = downstream,
type = type,
by = by,
TxDb = TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand = ignore_strand)
}
if (!(missingArg(conf) || is.na(conf))){
p <- plotPeakProf(tagMatrix = tagMatrix,
conf = conf,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
...)
} else {
p <- plotPeakProf(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
facet= facet,
free_y = free_y,
...)
}
return(p)
}
##' plot the profile of peaks in two or more windows
##'
##'
##' This function comes from \url{https://github.com/YuLab-SMU/ChIPseeker/issues/189}
##'`
##' \code{plotPeakProf_MultiWindows()} is almost the same as \code{plotPeakProf2()}, having
##' the main difference of accepting two or more granges objects. Accepting more
##' granges objects can help compare the same peaks in different windows.
##'
##' \code{TxDb} parameter can accept txdb object.
##' But many regions can not be obtained by txdb object. In this case,
##' Users can provide self-made granges served the same role
##' as txdb object and pass to \code{TxDb} object.
##'
##' \code{by} the features of interest.
##'
##' (1) if users use \code{txdb}, \code{by} can be one of 'gene', 'transcript', 'exon',
##' 'intron' , '3UTR' , '5UTR', 'UTR'. These features can be obtained by functions from txdb object.
##'
##' (2) if users use self-made granges object, \code{by} can be everything. Because this \code{by}
##' will not pass to functions to get features, which is different from the case of using
##' txdb object. This \code{by} is only used to made labels showed in picture.
##'
##' \code{type} means the property of the region. one of the "start site",
##' "end site" and "body".
##'
##' \code{upstream} and \code{downstream} parameter have different usages:
##'
##' (1) if \code{type == 'body'}, \code{upstream} and \code{downstream} can use to extend
##' the flank of body region.
##'
##' (2) if \code{type == 'start_site'/'end_site'}, \code{upstream} and \code{downstream} refer to
##' the upstream and downstream of the start_site or the end_site.
##'
##' \code{weightCol} refers to column in peak file. This column acts as a weight value. Details
##' see \url{https://github.com/YuLab-SMU/ChIPseeker/issues/15}
##'
##' \code{nbin} refers to the number of bins. \code{getTagMatrix()} provide a binning method
##' to get the tag matrix.
##'
##' There are two ways input a list of window.
##'
##' (1) Users can input a list of self-made granges objects
##'
##' (2) Users can input a list of \code{by} and only one \code{type}. In this way,
##' \code{plotPeakProf_MultiWindows()} can made a list of window from txdb object based on \code{by} and \code{type}.
##'
##' Warning:
##'
##' (1) All of these window should be the same type. It means users can only
##' compare a list of "start site"/"end site"/"body region" with the same upstream
##' and downstream.
##'
##' (2) So it will be only one \code{type} and several \code{by}.
##'
##' (3) Users can make window by txdb object or self-made granges object. Users can only
##' choose one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR' or 'UTR' in the
##' way of using txdb object. User can input any \code{by} in the way of using
##' self-made granges object.
##'
##' (4) Users can mingle the \code{by} designed for the two ways. \code{plotPeakProf_MultiWindows} can
##' accpet the hybrid \code{by}. But the above rules should be followed.
##'
##'
##' @title plotPeakProf_MultiWindows
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object or self-made granges objects
##' @param upstream upstream position
##' @param downstream downstream position
##' @param by feature of interest
##' @param type one of "start_site", "end_site", "body"
##' @param windows_name the name for each window, which will also be showed in the picture as labels
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param verbose print message or not
##' @param nbin the amount of bines
##' @param ignore_strand ignore the strand information or not
##' @param ... additional parameter
##' @return ggplot object
plotPeakProf_MultiWindows <- function(peak,
upstream,
downstream,
conf,
by,
type,
windows_name = NULL,
weightCol = NULL,
TxDb = NULL,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet = "row",
free_y = TRUE,
verbose = TRUE,
nbin = NULL,
ignore_strand = FALSE,
...){
conf <- if(missingArg(conf)) NA else conf
upstream <- if(missingArg(upstream)) NULL else upstream
downstream <- if(missingArg(downstream)) NULL else downstream
## check type
if(length(type) != 1){
stop("It should be only one type...")
}
## make the window name
if (is.null(windows_name)) {
nn <- by
warning("set the name automatically to ", paste(nn, collapse=' '))
windows_name <- nn
}else{
if (length(windows_name) != length(by)) {
stop("the length of the window name and the by should be equal...")
}
}
if ( is(peak, "list") ) {
tagMatrix <- lapply(peak, getTagMatrix2,
upstream=upstream,
downstream=downstream,
windows_name=windows_name,
type=type,
by=by,
TxDb=TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
} else {
tagMatrix <- getTagMatrix2(peak=peak,
upstream=upstream,
downstream=downstream,
windows_name=windows_name,
type=type,
by=by,
TxDb=TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
}
if (!(missingArg(conf) || is.na(conf))){
p <- plotMultiProf(tagMatrix = tagMatrix,
conf = conf,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
...)
} else {
p <- plotMultiProf(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
facet= facet,
free_y = free_y,
...)
}
return(p)
}
##' internal function for plotPeakProf_MultiWindows
##'
##' @param tagMatrix tagMatrix
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param ... additional parameter
plotMultiProf <- function(tagMatrix,
conf,
xlab="Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="none",
free_y = TRUE,
...){
if(is(tagMatrix[[1]][[1]],"matrix")){
upstream <- attr(tagMatrix[[1]][[1]], 'upstream')
downstream <- attr(tagMatrix[[1]][[1]], 'downstream')
# attr(tagMatrix, 'type') <- attr(tagMatrix[[1]][[1]], 'type')
# attr(tagMatrix, 'is.binning') <- attr(tagMatrix[[1]][[1]], 'is.binning')
binFlag <- attr(tagMatrix[[1]][[1]], 'is.binning')
type <- attr(tagMatrix[[1]][[1]], 'type')
}else{
upstream <- attr(tagMatrix[[1]], 'upstream')
downstream <- attr(tagMatrix[[1]], 'downstream')
binFlag <- attr(tagMatrix[[1]], 'is.binning')
type <- attr(tagMatrix[[1]], 'type')
}
if(type == "body"){
label <- c("SS","TS")
}else if(type == "start_site"){
label <- "SS"
}else{
label <- "TS"
}
if(binFlag){
if (!(missingArg(conf) || is.na(conf))){
plotMultiProf.binning(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
conf = conf,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}else{
plotMultiProf.binning(tagMatrix = tagMatrix,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}
}else{
xlim <- c(-upstream, downstream)
if (!(missingArg(conf) || is.na(conf))){
plotMultiProf.normal(tagMatrix = tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
conf = conf,
facet = facet,
free_y = free_y,
origin_label = label,
...)
}else{
plotMultiProf.normal(tagMatrix = tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = label,
...)
}
}
}
##' internal function
##'
##' @param tagMatrix tagMatrix
##' @param xlim xlim
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param origin_label the label of the center
##' @param verbose print message or not
##' @param ... additional parameter
plotMultiProf.normal <- function(tagMatrix, xlim,
xlab="Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet="none",
free_y = TRUE,
origin_label = "TSS",
verbose = TRUE,
...) {
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
if (verbose) {
cat(">> plotting figure...\t\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
conf <- if(missingArg(conf)) NA else conf
if (!(missingArg(conf) || is.na(conf))){
p <- plotMultiProf.normal.internal(tagMatrix = tagMatrix,
conf = conf,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = origin_label,
...)
} else {
p <- plotMultiProf.normal.internal(tagMatrix,
xlim = xlim,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
origin_label = origin_label,
...)
}
return(p)
}
##' internal function
##'
##'
##' @param tagMatrix tagMatrix
##' @param xlim xlim
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param origin_label the label of the center
##' @param ... additional parameter
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 geom_line
##' @importFrom ggplot2 geom_vline
##' @importFrom ggplot2 geom_ribbon
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 scale_color_manual
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 theme_bw
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 facet_grid
plotMultiProf.normal.internal <- function(tagMatrix, conf,
xlim = c(-3000,3000),
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="row",
free_y = TRUE,
origin_label,
...) {
listFlag <- FALSE
if (is.null(attr(tagMatrix[[1]],'upstream'))) {
if ( is.null(names(tagMatrix)) ) {
nn <- paste0("peak", seq_along(tagMatrix))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(tagMatrix) <- nn
## stop("tagMatrix should be a named list...")
}
listFlag <- TRUE
}
if ( listFlag ) {
facet <- match.arg(facet, c("none", "row", "column"))
if ( (xlim[2]-xlim[1]+1) != ncol(tagMatrix[[1]][[1]]) ) {
stop("please specify appropreate xcoordinations...")
}
} else {
if ( (xlim[2]-xlim[1]+1) != ncol(tagMatrix[[1]]) ) {
stop("please specify appropreate xcoordinations...")
}
}
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
##
conf <- if(missingArg(conf)) NA else conf
pos <- value <- .id <- Lower <- Upper <- NULL
if ( listFlag ) {
tagCount <- lapply(as.list(names(tagMatrix)), function(x){
tmp <- tagMatrix[[x]]
tagCount_tmp <- lapply(as.list(names(tmp)),function(x){
result <- getTagCount(tmp[[x]], xlim = xlim, conf = conf, ...)
result$type <- x
return(result)
})
tagCount_tmp <- list_to_dataframe(tagCount_tmp)
return(tagCount_tmp)
})
names(tagCount) <- names(tagMatrix)
tagCount <- list_to_dataframe(tagCount)
tagCount$.id <- factor(tagCount$.id, levels=names(tagMatrix))
p <- ggplot(tagCount, aes(pos, group=type, color=type))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = type),
linetype = 0, alpha = 0.2)
}
} else {
tagCount <- lapply(as.list(names(tagMatrix)), function(x){
result <- getTagCount(tagMatrix[[x]], xlim = xlim, conf = conf, ...)
result$type <- x
return(result)
})
tagCount <- do.call("rbind",tagCount)
p <- ggplot(tagCount, aes(x = pos))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper,fill = type),
linetype = 0, alpha = 0.2)
}
}
p <- p + geom_line(aes(y = value,color = type))
if ( 0 > xlim[1] && 0 < xlim[2] ) {
p <- p + geom_vline(xintercept=0,
linetype="longdash")
p <- p + scale_x_continuous(breaks=c(xlim[1], floor(xlim[1]/2),
0,
floor(xlim[2]/2), xlim[2]),
labels=c(paste0(xlim[1],"bp"), paste0(floor(xlim[1]/2),"bp"),
origin_label,
paste0(floor(xlim[2]/2),"bp"), paste0(xlim[2], "bp")))
}
if (listFlag) {
# cols <- getCols(length(tagMatrix[[1]]))
# p <- p + scale_color_manual(values=cols)
if (facet == "row") {
if (free_y) {
p <- p + facet_grid(.id ~ ., scales = "free_y")
} else {
p <- p + facet_grid(.id ~ .)
}
} else if (facet == "column") {
if (free_y) {
p <- p + facet_grid(. ~ .id, scales = "free_y")
} else {
p <- p + facet_grid(. ~ .id)
}
}
}
p <- p+xlab(xlab)+ylab(ylab)
p <- p + theme_bw() + theme(legend.title=element_blank())
# if(facet != "none") {
# p <- p + theme(legend.position="none")
# }
return(p)
}
##' internal function
##'
##' @param tagMatrix tagMatrix
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param upstream the upstream extension
##' @param downstream the downstream extension
##' @param label the label of the center
##' @param ... additional parameter
plotMultiProf.binning <- function(tagMatrix,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
conf,
facet ="none",
free_y = TRUE,
upstream = NULL,
downstream = NULL,
label,
...) {
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
conf <- if(missingArg(conf)) NA else conf
if (!(missingArg(conf) || is.na(conf))){
p <- plotMultiProf.binning.internal(tagMatrix ,
conf = conf,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
} else {
p <- plotMultiProf.binning.internal(tagMatrix ,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
upstream = upstream,
downstream = downstream,
label = label,
...)
}
return(p)
}
##' internal function
##'
##' @param tagMatrix tagMatrix
##' @param xlab xlab
##' @param ylab ylab
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param upstream the upstream extension
##' @param downstream the downstream extension
##' @param label the label of the center
##' @param ... additional parameter
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 geom_line
##' @importFrom ggplot2 geom_vline
##' @importFrom ggplot2 geom_ribbon
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 scale_color_manual
##' @importFrom ggplot2 xlab
##' @importFrom ggplot2 ylab
##' @importFrom ggplot2 theme_bw
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 facet_grid
##' @importFrom ggplot2 rel
plotMultiProf.binning.internal <- function(tagMatrix,
conf,
xlab = "Genomic Region (5'->3')",
ylab = "Peak Count Frequency",
facet="none",
free_y = TRUE,
upstream = NULL,
downstream = NULL,
label,
...) {
listFlag <- FALSE
if (is(tagMatrix[[1]][[1]],"matrix")) {
if ( is.null(names(tagMatrix)) ) {
nn <- paste0("peak", seq_along(tagMatrix))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(tagMatrix) <- nn
## stop("tagMatrix should be a named list...")
}
listFlag <- TRUE
}
if(listFlag){
nbin <- dim(tagMatrix[[1]][[1]])[2]
type <- attr(tagMatrix[[1]][[1]], 'type')
}else{
nbin <- dim(tagMatrix[[1]])[2]
type <- attr(tagMatrix[[1]], 'type')
}
xlim <- c(1,nbin)
if ( listFlag ) {
facet <- match.arg(facet, c("none", "row", "column"))
}
## S4Vectors change the behavior of ifelse
## see https://support.bioconductor.org/p/70871/
##
## conf <- ifelse(missingArg(conf), NA, conf)
##
conf <- if(missingArg(conf)) NA else conf
pos <- value <- .id <- Lower <- Upper <- NULL
if ( listFlag ) {
tagCount <- lapply(as.list(names(tagMatrix)), function(x){
tmp <- tagMatrix[[x]]
tagCount_tmp <- lapply(as.list(names(tmp)),function(x){
result <- getTagCount(tmp[[x]], xlim = xlim, conf = conf, ...)
result$type <- x
return(result)
})
tagCount_tmp <- list_to_dataframe(tagCount_tmp)
return(tagCount_tmp)
})
names(tagCount) <- names(tagMatrix)
tagCount <- list_to_dataframe(tagCount)
tagCount$.id <- factor(tagCount$.id, levels=names(tagMatrix))
p <- ggplot(tagCount, aes(pos, group=type, color=type))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper, fill = type),
linetype = 0, alpha = 0.2)
}
} else {
tagCount <- lapply(as.list(names(tagMatrix)), function(x){
result <- getTagCount(tagMatrix[[x]], xlim = xlim, conf = conf, ...)
result$type <- x
return(result)
})
tagCount <- do.call("rbind",tagCount)
p <- ggplot(tagCount, aes(pos,group=type,color=type))
if (!(is.na(conf))) {
p <- p + geom_ribbon(aes(ymin = Lower, ymax = Upper,fill = type),
linetype = 0, alpha = 0.2)
}
}
p <- p + geom_line(aes(y = value,color = type))
## x_scale for genebody
if(type == 'body'){
## x_scale for gene body with no flank extension
if(is.null(upstream)){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(label[1],
"25%",
"50%",
"75%",
label[2]))
}
## x_scale for flank extension by relative value
if(inherits(upstream, 'rel')){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+25)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+50)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+75)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
nbin),
labels=c(paste0("-",as.numeric(upstream)*100,"%"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0("+",as.numeric(downstream)*100,"%")))
p <- p + geom_vline(xintercept=floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
linetype="longdash")
p <- p + geom_vline(xintercept=floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
linetype="longdash")
}
## x_scale for flank extension by absolute value
if(!is.null(upstream) & !inherits(upstream, 'rel')){
upstreamPer <- floor(upstream/1000)*0.1
downstreamPer <- floor(downstream/1000)*0.1
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.25)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.5)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.75)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
nbin),
labels=c(paste0("-",upstream,"bp"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0(downstream,"bp")))
p <- p + geom_vline(xintercept=floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
linetype="longdash")
p <- p + geom_vline(xintercept=floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
linetype="longdash")
}
}
## x_scale for start region
if(type != 'body'){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(paste0("-",upstream,"bp"),
paste0("-",floor(upstream*0.5),"bp"),
label,
paste0(floor(downstream*0.5),"bp"),
paste0(downstream,"bp")))
p <- p + geom_vline(xintercept=floor(nbin*0.5),
linetype="longdash")
}
if (listFlag) {
if (facet == "row") {
if (free_y) {
p <- p + facet_grid(.id ~ ., scales = "free_y")
} else {
p <- p + facet_grid(.id ~ .)
}
} else if (facet == "column") {
if (free_y) {
p <- p + facet_grid(. ~ .id, scales = "free_y")
} else {
p <- p + facet_grid(. ~ .id)
}
}
}
p <- p+xlab(xlab)+ylab(ylab)
p <- p + theme_bw() + theme(legend.title=element_blank())
# if(facet != "none") {
# p <- p + theme(legend.position="none")
# }
return(p)
}
##' plot the heatmap of tagMatrix
##'
##'
##' @title tagHeatmap
##' @param tagMatrix tagMatrix or a list of tagMatrix
##' @param xlab xlab
##' @param ylab ylab
##' @param title title
##' @param palette palette to be filled in,details see \link[ggplot2]{scale_colour_brewer}
##' @param nrow the nrow of plotting a list of peak
##' @param ncol the ncol of plotting a list of peak
##' @return figure
##' @export
##' @author G Yu
tagHeatmap <- function(tagMatrix,
xlab="",
ylab="",
title=NULL,
palette="RdBu",
nrow = NULL,
ncol = NULL) {
listFlag <- FALSE
if (is(tagMatrix, "list")) {
listFlag <- TRUE
}
peakHeatmap.internal2(tagMatrix = tagMatrix,
listFlag = listFlag,
palette = palette,
xlab = xlab,
ylab = ylab,
title = title,
ncol = ncol,
nrow = nrow)
}
##' plot the heatmap of peaks
##'
##'
##' @title peakHeatmap
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param xlab xlab
##' @param ylab ylab
##' @param title title
##' @param palette palette to be filled in,details see \link[ggplot2]{scale_colour_brewer}
##' @param verbose print message or not
##' @param by one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'
##' @param type one of "start_site", "end_site", "body"
##' @param nbin the amount of nbines
##' @param ignore_strand ignore the strand information or not
##' @param windows a collection of region
##' @param nrow the nrow of plotting a list of peak
##' @param ncol the ncol of plotting a list of peak
##' @return figure
##' @export
##' @author G Yu
peakHeatmap <- function(peak, weightCol=NULL, TxDb=NULL,
upstream=1000, downstream=1000,
xlab="", ylab="", title=NULL,
palette=NULL, verbose=TRUE,
by="gene", type="start_site",
nbin = NULL,ignore_strand = FALSE,
windows,ncol = NULL, nrow = NULL) {
listFlag <- FALSE
if ( is(peak, "list") ) {
listFlag <- TRUE
if (is.null(names(peak)))
stop("peak should be a peak file or a name list of peak files...")
}
if (verbose) {
cat(">> preparing promoter regions...\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
if (verbose) {
cat(">> preparing tag matrix...\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
if(missing(windows)){
windows <- getBioRegion(TxDb=TxDb,
upstream=upstream,
downstream=downstream,
by=by,
type=type)
}
if (listFlag) {
tagMatrix <- lapply(peak, getTagMatrix,
weightCol=weightCol,
windows = windows,
upstream=upstream,
downstream=downstream,
TxDb = TxDb,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
names(tagMatrix) <- names(peak)
} else {
tagMatrix <- getTagMatrix(peak,
weightCol=weightCol,
windows = windows,
TxDb = TxDb,
upstream=upstream,
downstream=downstream,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
}
if (verbose) {
cat(">> generating figure...\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
xlim <- NULL
p <- peakHeatmap.internal2(tagMatrix = tagMatrix,
listFlag = listFlag,
palette = palette,
xlab = xlab,
ylab = ylab,
title = title,
nrow = nrow,
ncol = ncol)
if (verbose) {
cat(">> done...\t\t\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
invisible(tagMatrix)
p
}
##' @importFrom aplot plot_list
peakHeatmap.internal2 <- function(tagMatrix,
listFlag,
palette,
xlab,
ylab,
title,
nrow,
ncol) {
if ( is.null(xlab) || is.na(xlab))
xlab <- ""
if ( is.null(ylab) || is.na(ylab))
ylab <- ""
if (listFlag) {
nc <- length(tagMatrix)
if ( is.null(palette) || is.na(palette) ) {
palette <- getPalette(nc)
} else if (length(palette) != nc) {
palette <- rep(palette[1], nc)
} else {
palette <- palette
}
if (is.null(title) || is.na(title))
title <- names(tagMatrix)
if (length(xlab) != nc) {
xlab <- rep(xlab[1], nc)
}
if (length(ylab) != nc) {
ylab <- rep(ylab[1], nc)
}
if (length(title) != nc) {
title <- rep(title[1], nc)
}
tmp <- list()
for (i in 1:nc) {
p <- peakHeatmap.internal(tagMatrix = tagMatrix[[i]],
palette = palette[i],
xlab = xlab[i],
ylab = ylab[i],
title= title[i])
p <- p + theme(plot.title = element_text(hjust = 0.5))
tmp[[i]] <- p
}
if(is.null(nrow) && is.null(ncol))
nrow <- 1
p <- plot_list(gglist = tmp,
ncol = ncol,
nrow = nrow)
return(p)
} else {
if (is.null(palette) || is.na(palette))
palette <- "RdBu"
if (is.null(title) || is.na(title))
title <- ""
peakHeatmap.internal(tagMatrix = tagMatrix,
palette = palette,
xlab = xlab,
ylab = ylab,
title = title)
}
}
##' @import BiocGenerics
##' @importFrom yulab.utils mat2df
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 aes
##' @importFrom ggplot2 geom_tile
##' @importFrom ggplot2 scale_fill_distiller
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 labs
##' @importFrom ggplot2 scale_x_continuous
peakHeatmap.internal <- function(tagMatrix,
palette="RdBu",
xlab="",
ylab="",
title="") {
upstream <- attr(tagMatrix, "upstream")
downstream <- attr(tagMatrix, "downstream")
binning_Flag <- attr(tagMatrix,"is.binning")
type <- attr(tagMatrix,"type")
body_Flag <- FALSE
if(type == "body"){
body_Flag <- TRUE
label <- attr(tagMatrix,"label")
}
if(binning_Flag){
nbin <- dim(tagMatrix)[2]
}
tagMatrix <- t(apply(tagMatrix, 1, function(x) x/max(x)))
ii <- order(rowSums(tagMatrix))
tagMatrix <- tagMatrix[ii,]
colnames(tagMatrix) <- seq_len(dim(tagMatrix)[2])
rownames(tagMatrix) <- seq_len(dim(tagMatrix)[1])
tagMatrix <- mat2df(tagMatrix)
colnames(tagMatrix) <- c("values","sample_ID","coordinate")
sample_ID <- coordinate <- NULL
p <- ggplot(tagMatrix, aes(x = coordinate,y = sample_ID)) +
geom_tile(aes(fill = values)) +
scale_fill_distiller(palette = palette) +
theme(axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.line.y = element_blank(),
panel.grid=element_blank(),
panel.background = element_blank()) +
labs(x = xlab, y = ylab, title = title)
if(body_Flag){
if(inherits(upstream, 'rel')){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+25)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+50)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+75)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
nbin),
labels=c(paste0("-",as.numeric(upstream)*100,"%"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0("+",as.numeric(downstream)*100,"%")))
}
if(is.null(upstream)){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(label[1],
"25%",
"50%",
"75%",
label[2]))
}
if(!is.null(upstream) && !inherits(upstream, 'rel')){
upstreamPer <- floor(upstream/1000)*0.1
downstreamPer <- floor(downstream/1000)*0.1
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.25)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.5)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.75)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
nbin),
labels=c(paste0("-",upstream,"bp"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0(downstream,"bp")))
}
p <- p + scale_y_continuous(expand = c(0,0))
return(p)
}
if(binning_Flag){
p <- p + scale_x_continuous(breaks = c(1,
floor(nbin*(downstream*0.5/(downstream+upstream))),
floor(nbin*(downstream/(downstream+upstream))),
floor(nbin*((downstream + upstream*0.5)/(downstream+upstream))),
nbin),
labels = c((-1*downstream),
floor(-1*downstream*0.5),
0,
floor(upstream*0.5),
upstream))
}else{
p <- p + scale_x_continuous(labels = function(x) x - upstream)
}
p <- p + scale_y_continuous(expand = c(0,0))
p
}
##' plot the heatmap of peaks align to a sets of regions
##'
##'
##' @title peakHeatmap
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param xlab xlab
##' @param ylab ylab
##' @param title title
##' @param palette palette to be filled in,details see \link[ggplot2]{scale_colour_brewer}
##' @param verbose print message or not
##' @param by one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'
##' @param type one of "start_site", "end_site", "body"
##' @param nbin the amount of nbines
##' @param ignore_strand ignore the strand information or not
##' @param windows_name the name for each window, which will also be showed in the picture as labels
##' @param nrow the nrow of plotting a list of peak
##' @param ncol the ncol of plotting a list of peak
##' @param facet_label_text_size the size of facet label text
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 aes
##' @importFrom ggplot2 geom_tile
##' @importFrom ggplot2 scale_fill_distiller
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 labs
##' @importFrom ggplot2 scale_x_continuous
##' @return figure
##' @export
peakHeatmap_multiple_Sets <- function(peak,
weightCol=NULL,
TxDb=NULL,
upstream=1000,
downstream=1000,
xlab="",
ylab="",
title=NULL,
palette=NULL,
verbose=TRUE,
by="gene",
type="start_site",
nbin = NULL,
ignore_strand = FALSE,
windows_name = NULL,
ncol = NULL,
nrow = NULL,
facet_label_text_size = 12){
listFlag <- FALSE
if ( is(peak, "list") ) {
listFlag <- TRUE
if (is.null(names(peak)))
stop("peak should be a peak file or a name list of peak files...")
}
if (verbose) {
cat(">> preparing promoter regions...\t",
format(Sys.time(), "%Y-%m-%d %X"), "\n")
}
## check type
if(length(type) != 1){
stop("It should be only one type...")
}
if(is.null(windows_name) && !is.null(names(TxDb)))
windows_name <- names(TxDb)
## make the window name
if (is.null(windows_name)) {
nn <- by
warning("set the name automatically to ", paste(nn, collapse=' '))
windows_name <- nn
}else{
if (length(windows_name) != length(by)) {
stop("the length of the window name and the by should be equal...")
}
}
if ( is(peak, "list") ) {
tagMatrix <- lapply(peak, getTagMatrix2,
upstream=upstream,
downstream=downstream,
windows_name=windows_name,
type=type,
by=by,
TxDb=TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
} else {
tagMatrix <- getTagMatrix2(peak=peak,
upstream=upstream,
downstream=downstream,
windows_name=windows_name,
type=type,
by=by,
TxDb=TxDb,
weightCol = weightCol,
nbin = nbin,
verbose = verbose,
ignore_strand= ignore_strand)
}
if(listFlag){
nc <- length(tagMatrix)
if ( is.null(palette) || is.na(palette) ) {
palette <- getPalette(nc)
} else if (length(palette) != nc) {
palette <- rep(palette[1], nc)
} else {
palette <- palette
}
if (is.null(title) || is.na(title))
title <- names(tagMatrix)
if (length(xlab) != nc) {
xlab <- rep(xlab[1], nc)
}
if (length(ylab) != nc) {
ylab <- rep(ylab[1], nc)
}
if (length(title) != nc) {
title <- rep(title[1], nc)
}
tmp <- list()
for (i in 1:nc) {
p <- peakHeatmap_multiple_Sets.internal(tagMatrix = tagMatrix[[i]],
upstream=upstream,
downstream=downstream,
xlab=xlab[[i]],
ylab=ylab[[i]],
title=title[[i]],
palette=palette[[i]],
ncol = ncol,
nrow = nrow,
facet_label_text_size = facet_label_text_size)
p <- p + theme(plot.title = element_text(hjust = 0.5))
tmp[[i]] <- p
}
if(is.null(nrow) && is.null(ncol))
nrow <- 1
p <- plot_list(gglist = tmp,
ncol = ncol,
nrow = nrow)
}else{
if (is.null(palette) || is.na(palette))
palette <- "RdBu"
if (is.null(title) || is.na(title))
title <- ""
p <- peakHeatmap_multiple_Sets.internal(tagMatrix = tagMatrix,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette,
ncol = ncol,
nrow = nrow,
facet_label_text_size = facet_label_text_size)
}
return(p)
}
##' @importFrom yulab.utils mat2df
##' @importFrom ggplot2 ggplot
##' @importFrom ggplot2 aes
##' @importFrom ggplot2 geom_tile
##' @importFrom ggplot2 scale_fill_distiller
##' @importFrom ggplot2 theme
##' @importFrom ggplot2 element_blank
##' @importFrom ggplot2 labs
##' @importFrom ggplot2 scale_x_continuous
##' @importFrom ggplot2 facet_grid
##' @importFrom ggplot2 element_text
##' @importFrom ggplot2 element_blank
peakHeatmap_multiple_Sets.internal <- function(tagMatrix,
upstream=1000,
downstream=1000,
xlab="",
ylab="",
title=NULL,
palette=NULL,
ncol = NULL,
nrow = NULL,
facet_label_text_size = 12){
binning_Flag <- attr(tagMatrix[[1]],"is.binning")
if(binning_Flag) nbin <- dim(tagMatrix[[1]])[2]
type <- attr(tagMatrix,"type")
body_Flag <- FALSE
if(attr(tagMatrix[[1]],"type") == "body"){
body_Flag <- TRUE
label <- attr(tagMatrix,"label")
}
name_of_list <- as.list(names(tagMatrix))
peak_list <- lapply(name_of_list,function(x){
tagMatrix[[x]] <- t(apply(tagMatrix[[x]], 1, function(x) x/max(x)))
ii <- order(rowSums(tagMatrix[[x]]))
tagMatrix[[x]] <- tagMatrix[[x]][ii,]
colnames(tagMatrix[[x]]) <- seq_len(dim(tagMatrix[[x]])[2])
rownames(tagMatrix[[x]]) <- seq_len(dim(tagMatrix[[x]])[1])
tagMatrix[[x]] <- mat2df(tagMatrix[[x]])
colnames(tagMatrix[[x]]) <- c("values","sample_ID","coordinate")
tagMatrix[[x]]$sample <- x
return(tagMatrix[[x]])
})
peak_df <- list_to_dataframe(peak_list)
sample_ID <- coordinate <- NULL
p <- ggplot(peak_df, aes(x = coordinate,y = sample_ID)) +
geom_tile(aes(fill = values)) +
scale_fill_distiller(palette = palette) +
theme(axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.line.y = element_blank(),
panel.grid=element_blank(),
panel.background = element_blank()) +
labs(x = xlab, y = ylab, title = title)
if(body_Flag){
if(inherits(upstream, 'rel')){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(as.numeric(upstream)*100/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+25)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+50)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+75)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
floor(nbin*((as.numeric(upstream)*100+100)/(100+(as.numeric(upstream)+as.numeric(downstream))*100))),
nbin),
labels=c(paste0("-",as.numeric(upstream)*100,"%"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0("+",as.numeric(downstream)*100,"%")))
}
if(is.null(upstream)){
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*0.25),
floor(nbin*0.5),
floor(nbin*0.75),
nbin),
labels=c(label[1],
"25%",
"50%",
"75%",
label[2]))
}
if(!is.null(upstream) && !inherits(upstream, 'rel')){
upstreamPer <- floor(upstream/1000)*0.1
downstreamPer <- floor(downstream/1000)*0.1
p <- p + scale_x_continuous(breaks=c(1,
floor(nbin*(upstreamPer/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.25)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.5)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+0.75)/(1+upstreamPer+downstreamPer))),
floor(nbin*((upstreamPer+1)/(1+upstreamPer+downstreamPer))),
nbin),
labels=c(paste0("-",upstream,"bp"),
label[1],
"25%",
"50%",
"75%",
label[2],
paste0(downstream,"bp")))
}
p <- p + facet_grid(sample ~ .,switch = "y",space = "free_y",scales = "free_y") +
theme(strip.text.y.left = element_text(color = "black",face = "bold",
size = facet_label_text_size),
strip.background = element_blank())
return(p)
}
if(binning_Flag){
p <- p + scale_x_continuous(breaks = c(1,
floor(nbin*(downstream*0.5/(downstream+upstream))),
floor(nbin*(downstream/(downstream+upstream))),
floor(nbin*((downstream + upstream*0.5)/(downstream+upstream))),
nbin),
labels = c((-1*downstream),
floor(-1*downstream*0.5),
0,
floor(upstream*0.5),
upstream))
}else{
p <- p + scale_x_continuous(breaks = c(1,
floor(downstream*0.5),
(downstream + 1),
(downstream + 1 + floor(upstream * 0.5)),
upstream+downstream+1),
labels = c((-1*downstream),
floor(-1*downstream*0.5),
0,
floor(upstream*0.5),
upstream))
}
p <- p + facet_grid(sample ~ .,switch = "y",scales = "free_y",space = "free") +
theme(strip.text.y.left = element_text(color = "black",face = "bold",
size = facet_label_text_size),
strip.background = element_blank()) +
scale_y_continuous(expand = c(0,0))
return(p)
}
##' plot peak heatmap and profile in a picture
##'
##'
##' @title peak_Profile_Heatmap
##' @param peak peak file or GRanges object
##' @param weightCol column name of weight
##' @param TxDb TxDb object
##' @param upstream upstream position
##' @param downstream downstream position
##' @param xlab xlab
##' @param ylab ylab
##' @param title title
##' @param palette palette to be filled in,details see \link[ggplot2]{scale_colour_brewer}
##' @param verbose print message or not
##' @param by one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'
##' @param type one of "start_site", "end_site", "body"
##' @param nbin the amount of nbines
##' @param ignore_strand ignore the strand information or not
##' @param windows_name the name for each window, which will also be showed in the picture as labels
##' @param nrow the nrow of plotting a list of peak
##' @param ncol the ncol of plotting a list of peak
##' @param facet_label_text_size the size of facet label text
##' @param conf confidence interval
##' @param facet one of 'none', 'row' and 'column'
##' @param free_y if TRUE, y will be scaled by AvgProf
##' @param height_proportion the proportion of profiling picture and heatmap
##' @importFrom aplot insert_bottom
##' @importFrom aplot plot_list
##' @export
peak_Profile_Heatmap <- function(peak,
weightCol=NULL,
TxDb=NULL,
upstream=1000,
downstream=1000,
xlab="",
ylab="",
title=NULL,
palette=NULL,
verbose=TRUE,
by="gene",
type="start_site",
nbin = NULL,
ignore_strand = FALSE,
windows_name = NULL,
ncol = NULL,
nrow = NULL,
facet_label_text_size = 12,
conf,
facet = "row",
free_y = TRUE,
height_proportion = 4){
conf <- if(missingArg(conf)) NA else conf
if(is(peak, "list")){
nc <- length(peak)
tmp <- list()
if ( is.null(names(peak)) ) {
nn <- paste0("peak", seq_along(peak))
warning("input is not a named list, set the name automatically to ", paste(nn, collapse=' '))
names(peak) <- nn
## stop("tagMatrix should be a named list...")
}
if(is.null(palette)) palette <- getPalette(nc)
if(is.null(title)) title_of_plot <- names(peak)
for (i in 1:nc) {
peak_profile <- plotPeakProf(peak = peak[[i]],
upstream = upstream,
downstream = downstream,
conf = conf,
by = by,
type = type,
windows_name = windows_name,
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
nbin = nbin,
ignore_strand = ignore_strand)
peak_profile <- peak_profile + labs(title = title_of_plot[i]) +
theme(plot.title = element_text(hjust = 0.5))
if(length(by) != 1){
peak_heatmap <- peakHeatmap_multiple_Sets(peak = peak[[i]],
weightCol=weightCol,
TxDb=TxDb,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette[[i]],
verbose=verbose,
by=by,
type=type,
nbin = nbin,
ignore_strand = ignore_strand,
windows_name = windows_name,
ncol = ncol,
nrow = nrow,
facet_label_text_size = facet_label_text_size)
}else{
peak_heatmap <- peakHeatmap(peak[[i]],
weightCol=weightCol,
TxDb=TxDb,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette[[i]],
verbose=verbose,
by=by,
type=type,
nbin = nbin,
ignore_strand = ignore_strand,
ncol = ncol,
nrow = nrow)
}
p <- peak_profile %>%
insert_bottom(peak_heatmap,height = height_proportion)
tmp[[i]] <- p
}
if (is.null(ncol) && is.null(nrow))
nrow <- 1
p <- plot_list(gglist = tmp,
ncol = ncol,
nrow = nrow)
return(p)
}
peak_profile <- plotPeakProf(peak = peak,
upstream = upstream,
downstream = downstream,
conf = conf,
by = by,
type = type,
windows_name = windows_name,
weightCol = weightCol,
TxDb = TxDb,
xlab = xlab,
ylab = ylab,
facet = facet,
free_y = free_y,
verbose = verbose,
nbin = nbin,
ignore_strand = ignore_strand)
if(length(by) != 1){
peak_heatmap <- peakHeatmap_multiple_Sets(peak = peak,
weightCol=weightCol,
TxDb=TxDb,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette,
verbose=verbose,
by=by,
type=type,
nbin = nbin,
ignore_strand = ignore_strand,
windows_name = windows_name,
ncol = ncol,
nrow = nrow,
facet_label_text_size = facet_label_text_size)
}else{
peak_heatmap <- peakHeatmap(peak = peak,
weightCol=weightCol,
TxDb=TxDb,
upstream=upstream,
downstream=downstream,
xlab=xlab,
ylab=ylab,
title=title,
palette=palette,
verbose=verbose,
by=by,
type=type,
nbin = nbin,
ignore_strand = ignore_strand,
ncol = ncol,
nrow = nrow)
}
p <- peak_profile %>%
insert_bottom(peak_heatmap,height = height_proportion)
return(p)
}
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