R/Functions_plotting_EICs.R
In mjhelf/Metaboseek: Metaboseek platform
Defines functions
legendplot
addLines
EICplot
groupPlot
EICtitles
EICgeneral
Documented in
addLines
EICgeneral
EICplot
EICtitles
groupPlot
legendplot
#' EICgeneral
#'
#' wrapper function to plot multiple EICs
#'
#'
#' @param rtmid vector of retention time values (not ranges). If length >1,
#' multiple plots are called (multiple pages in pdf file)
#' @param mzmid vector of mz values (not ranges).
#' Has to be same length as \code{rtmid}
#' @param glist a named list of grouped file names
#' (as supplied in $grouping of rawLayout objects)
#' @param cols integer, number of columns in plot. if NULL,
#' grid can be defined externally
#' @param colrange character(1), color range function used for line colors,
#' OR a list of data.frames, see \code{Details}
#' @param transparency numeric(1), alpha (range 0..1) for transparency of lines
#' @param RTall if TRUE, entire RT range will be plotted
#' @param TICall if TRUE, TIC will be plotted instead of EIC
#' @param rtw retention time window +/- rtmid in seconds that will be plotted
#' @param ppm mz window +/- mzmid in ppm that will be plotted
#' @param rdata named list of xcmsRaw objects
#' @param pdfFile character - if not NULL, plotting result will be saved in a
#' pdf file with this name.
#' @param leadingTIC if TRUE, a TIC plot is made before the EIC plots
#' (e.g. as first page of pdf file)
#' @param midline if TRUE, dotted vertical line should be plotted at feature rt
#' @param lw line width for plot lines
#' @param yzoom zoom factor into y-axis
#' @param cx character expansion factor (font size)
#' @param adducts numeric() of mass shifts to be added to feature masses
#' @param RTcorrect if not NULL, this RTcorr object will be used to
#' adjust retention times.
#' @param importEIC a \code{\link{multiEICplus}()} output object to plot here, If NULL,
#' \code{multiEICplus()} is called with the other supplied parameters
#' @param globalYmax if TRUE, all EICs are scaled to the maximum value across all
#' plotting groups instead of the maximum within each group
#' @param subtitles subtitles for each EIC, must be character of
#' same length as rtmid and mzmid or NULL
#' @param raise if TRUE, EIC will be plotted with y axis going to
#' -0.02*max(ylim) so that EICs with 0 intensity are visible.
#' @param relPlot if TRUE, y-axis will show relative intensities
#' @param margins manual setting for plot margins (par$mar)
#' @param ylabshift shift horizontal position of y axis label
#' @param RescaleExclude character(), exclude this group from rescaling, or NULL to use all
#'
#' @return sends a grouped EIC plot to the current plotting device, or
#' generates a .pdf file
#'
#' @details
#' \describe{
#' \item{colrange}{A named list with the same structure as \code{glist},
#' but with a data.frame in each list element with row order corresponding to
#' items in the list elements of \code{glist} and columns \code{color} and \code{label},
#' specifying the EIC color and legend label for each EIC trace.
#' }
#' }
#'
#' @export
EICgeneral <- function(rtmid,
mzmid,
glist,
cols = NULL,
colrange = "Mseek.colors",
transparency = 1,
RTall = FALSE,
TICall = FALSE,
rtw = 30,
ppm = 5,
rdata,
pdfFile = "plotOutput.pdf",
leadingTIC = T,
lw = 1,
adducts = c(0),
cx = 1,
midline = T,
yzoom = 1,
RTcorrect = NULL,
importEIC = NULL,
globalYmax = FALSE,
subtitles = NULL,
raise = F,
relPlot = F,
margins = NULL,
ylabshift = 0,
RescaleExclude = NULL
){
#number of plot rows
if(!is.null(cols)){
rows <- ceiling(length(glist)/cols)
}else{
rows <-1}
if(!is.list(colrange)){
#make color scales for each group, color shades based on group with most members
colvec <- do.call(colrange,
list(n=max(sapply(glist,length)), alpha = transparency))
colrs <- list()
for(i in 1:length(glist)){
colrs[[i]] <- data.frame(color = colvec[1:length(glist[[i]])],
label = sub("^([^.]*).*", "\\1",basename(glist[[i]])),
stringsAsFactors = FALSE)
}}
else{
colrs <- colrange
}
# print(colrs)
#generate rt boundary df
if(any(RTall, is.null(rtmid))){ # any can handle NULL, seems more flexible than ||
rtmid <- NULL
rtx <- NULL
}else{
rtx <- data.frame(rtmin = rtmid - rtw,
rtmax = rtmid + rtw)
}
#generate mz boundary df
if(any(TICall, is.null(mzmid)) ){
mzmid <- if(!is.null(rtmid)){rep(100,length(rtmid))}else{100}
mzx <- data.frame(mzmin = mzmid-1,
mzmax = mzmid+1)
titx <- if(!is.null(rtmid)){rep("TICs",length(rtmid))}else{"TICs"}
tictog <- TRUE
}else{
tictog <- FALSE
mzx <- data.frame(mzmin = mzmid - mzmid*ppm*1e-6,
mzmax = mzmid + mzmid*ppm*1e-6)
titx <- EICtitles(mzmid, rtmid, ppm)
}
if(length(titx) != length(subtitles)){ subtitles <-NULL}
#optionally export to pdf
if(!is.null(pdfFile)){
if(is.null(cols)){
rows <- ceiling(length(glist)/5)
cols <-1}
pdf(pdfFile,
6*cols,
6*ceiling(length(glist)/cols)+2
)}
#optionally plot TICs first (page 1 in pdf)
if(leadingTIC){
EICsTIC <- multiEIC(rawdata= rdata[basename(names(rdata)) %in% basename(unlist(glist))],
mz = mzx[1,],
rt = NULL,
rnames = "1", #major item names
byFile = F,#if true, table will be sorted by rawfile, otherwise by feature
RTcorr = RTcorrect
)
yl <- if(!is.null(globalYmax)
&& globalYmax){matrix(c(rep(0, length(EICsTIC)),
sapply(EICsTIC, function(x){ max(unlist(x[,"tic"])) })), ncol = 2, byrow = F)}else{NULL}
groupPlot(EIClist = EICsTIC,
grouping = glist,
plotProps = list(TIC = T, #settings for single plots
cx = cx,
colr = colrs,
lw = lw,
midline = NULL,
ylim = yl, #these should be data.frames or matrices of nrow = number of plotted features
xlim = NULL,
yzoom = 1),
compProps = list(mfrow=c(rows,cols), #par options for the composite plot
oma=c(0,2,4,0),
xpd=NA, bg="white",
header = "TICs",
header2 = NULL,
pdfFile = NULL,
pdfHi = 6*rows,
pdfWi = 6*cols,
cx = cx,
adductLabs = 0),
raise,
relPlot,
margins,
ylabshift
)
}
if(is.null(importEIC)){
EICs <- multiEICplus(rawdata= rdata[basename(names(rdata)) %in% basename(unlist(glist))],
mz = mzx,
rt = if(is.null(RTcorrect)){rtx}else{NULL},
rnames = row.names(mzmid), #major item names
byFile = F, #if true, table will be sorted by rawfile, otherwise by feature
adducts,
RTcorr = RTcorrect
)}
else{
EICs <- importEIC
}
if(!is.null(RescaleExclude)
&& length(na.omit(match(RescaleExclude,names(glist)))) > 0
&& length(na.omit(match(RescaleExclude,names(glist)))) < length(glist)){
excludedfiles <- unlist(glist[match(RescaleExclude,names(glist))])
}else{
excludedfiles <- character(0)
}
if(TICall){
if(is.null(rtx) || length(EICs) %% nrow(rtx) != 0 ){
yl <- if(!is.null(globalYmax)
&& globalYmax){matrix(c(rep(0, length(EICs)),
sapply(EICs, function(x){ max(unlist(x[,"tic"])) })), ncol = 2, byrow = F)}else{NULL}
}
else{
suppressWarnings({
yl <- if(!is.null(globalYmax)
&& globalYmax){matrix(c(rep(0, length(EICs)),
mapply(function(x, rt){ max(unlist(x[,"tic"])[unlist(x[,"rt"]) >= max(c(min(rt),min(unlist(x[,"rt"])))) & unlist(x[,"rt"]) <= min(c(max(rt),max(unlist(x[,"rt"]))))])}, x = EICs, rt = as.list(as.data.frame(t(as.matrix(rtx)))) )), ncol = 2, byrow = F)}else{NULL}
}) #warnings occur if all scans are out of given rt range
}
}else{
#make sure the EICs all get scaled to their highest intensity across all adducts
if(is.null(rtx) || length(EICs) %% nrow(rtx) != 0 ){
maxys <- Biobase::rowMax(matrix(sapply(EICs, function(x){ max(unlist(x[which(!rownames(x) %in% excludedfiles),"intensity"])) }), ncol = length(adducts), byrow = F))
}else{
suppressWarnings({
maxys <- Biobase::rowMax(matrix(mapply(function(x, rt){
subsel <- which(!rownames(x) %in% excludedfiles)
max(unlist(x[subsel,"intensity"])[unlist(x[subsel,"rt"]) >= max(c(min(rt),min(unlist(x[subsel,"rt"]))))
& unlist(x[subsel,"rt"]) <= min(c(max(rt),max(unlist(x[subsel,"rt"]))))])},
x = EICs, rt = as.list(as.data.frame(t(as.matrix(rtx)))) ), ncol = length(adducts), byrow = F))
}) #warnings occur if all scans are out of given rt range
}
yl <- if(!is.null(globalYmax) && globalYmax){matrix(c(rep(0, length(EICs)),rep(maxys, length(adducts))), ncol = 2, byrow = F)}else{NULL}
}
groupPlot(EIClist = EICs,
grouping = glist,
plotProps = list(TIC = tictog, #settings for single plots
cx = cx,
colr = colrs,
xlim = rtx,
ylim = yl, #these should be data.frames or matrices of nrow = number of plotted features
lw = lw,
midline = if(midline){rtmid}else{NULL},
yzoom = yzoom),
compProps = list(mfrow=c(rows,cols), #par options for the composite plot
oma=c(0,2,4,0),
xpd=NA, bg="white",
header = titx,
header2 = subtitles,
pdfFile = NULL,
pdfHi = 6*rows,
pdfWi = 6*cols,
cx = cx,
adductLabs = adducts),
raise,
relPlot,
margins,
ylabshift,
RescaleExclude
)
if(!is.null(pdfFile)){dev.off()}
}
#' EICtitles
#'
#' helper function to generate titles for EICgeneral
#'
#'
#' @param rts vector of retention time values (not ranges)
#' @param mzs vector of mz values (not ranges)
#' @param ppm mz window +/- mzmid in ppm that will be plotted
#'
#' @return a character vector with plot titles of same length as
#' \code{rts} and \code{mzs}
#'
EICtitles <- function(mzs, rts, ppm){
if(!is.null(ppm)){
numbs <- matrix(mapply(sprintf,matrix(c(mzs,
mzs-mzs*ppm*1e-6,
mzs+mzs*ppm*1e-6),ncol=3),
MoreArgs = list(fmt = "%.5f")),
ncol=3)
titx <- paste0('m/z range: ',numbs[,1], " +/- ",
format(ppm, scientific = F),
" ppm (", numbs[,2]," - ", numbs[,3],")",
if(!is.null(rts)){
paste0(
" @ RT: ", sprintf( "%.2f", rts/60), " min",
" (", sprintf("%.1f", rts)," sec)")})
}
else{
numbs <- sprintf("%.5f", mzs)
titx <- paste0('m/z: ',numbs,
if(!is.null(rts)){
paste0(
" @ RT: ", sprintf( "%.2f", rts/60), " min",
" (", sprintf("%.1f", rts)," sec)")})
}
return(titx)
}
#' groupPlot
#'
#' generate multiple EICs on one page
#'
#'
#' @param EIClist list of EICs from \code{\link{multiEIC}()} or \code{\link{multiEICplus}()}
#' @param grouping a named list of grouped file names (as supplied in $grouping of rawLayout objects)
#' @param plotProps a list of settings for the individual plots, see \code{Details}
#' @param compProps layoout options for the composite plot, see \code{Details}
#' @param raise if TRUE, EIC will be plotted with y axis going to -0.02*max(ylim) so that EICs with 0 intensity are visible.
#' @param relPlot if TRUE, y-axis will show relative intensities
#' @param margins manual setting for plot margins (par$mar)
#' @param ylabshift shift horizontal position of y axis label
#' @param RescaleExclude character(), exclude this group from rescaling, or NULL to use all
#'
#' @return sends a grouped EIC plot to the current plotting device
#'
#' @details
#' \describe{
#' \item{plotProps}{A list with these elements:
#' \itemize{
#' \item \code{TIC} if TRUE, TIC instead of EIC
#' \item \code{cx} numeric(1) font size (character expansion) factor
#' \item \code{colr} color range (actual vector of color values)
#' \item \code{ylim} data.frame or matrix of nrow = number of plotted features,
#' with min and max visible rt value (in seconds) for each feature
#' \item \code{xlim} data.frame or matrix of nrow = number of plotted features,
#' with min and max visible intensity value for each feature
#' \item \code{midline} numeric() of y-axis positions where a dotted vertical
#' line should be plotted
#' \item \code{lw} line width for plot lines
#' \item \code{yzoom} zoom factor into y-axis
#' }
#' }
#' \item{compProps}{
#' \itemize{
#' \item \code{mfrow} integer(2) rows and columns for plotting (cf. par(), mfrow)
#' \item \code{oma} numeric(4) outer margins (cf. par(), oma)
#' \item \code{xpd} drawing outside of plot region, cf. par(), xpd
#' \item \code{bg} background color, cf. par(), bg
#' \item \code{header} First (title) line of composite plot
#' \item \code{header2} Subtitle line of composite plot
#' \item \code{pdfFile} character - if not NULL, plotting result will be saved in a pdf file with this name.
#' \item \code{pdfHi} pdf height in inches
#' \item \code{pdfWi} pdf width in inches
#' \item \code{cx} numeric(1) font size (character expansion) factor
#' \item \code{adductLabs} adduct labels (nonfunctional)
#' }
#' }
#' }
#'
#' @export
groupPlot <- function(EIClist,
grouping,
plotProps = list(TIC = TRUE, #settings for single plots
cx = 1,
colr = topo.colors(nrow(EIClist[[1]]), alpha=1),
ylim = NULL, #these should be data.frames or matrices of nrow = number of plotted features
xlim = NULL,
lw = 1,
midline = 100,
yzoom = 1),
compProps = list(mfrow=c(1,2), #par options for the composite plot
oma=c(0,2,8,0),
xpd=NA, bg=NA,
header = paste0(names(EIClist)),
header2 = NULL,
pdfFile = NULL,
pdfHi = 6,
pdfWi = 12,
cx = 1,
adductLabs = c("0","1","2")),
raise = F,
relPlot = F,
margins = NULL,
ylabshift = 0,
RescaleExclude = NULL
){
#majoritem is the EIClist top level (typically by mz, but could be)
if(!is.null(compProps$pdfFile)){pdf(compProps$pdfFile,compProps$pdfWi,compProps$pdfHi)}
if(!is.null(compProps$header)){
autosize <- compProps$cx*1.5
while(max(strwidth(compProps$header, units = "figure", cex = autosize, font = 2)) > 1){
autosize <- autosize*0.975
}
}
nrowcheck <- if(!is.null(nrow(EIClist))){nrow(EIClist)}else {1}
for(majoritem in c(1:nrowcheck)){
#adductLabs legend does not work yet
#if(length(compProps$adductLabs)>1){compProps$mfrow[1] <- compProps$mfrow[1]+1}
if(length(compProps$mfrow) > 1){
par(mfrow=compProps$mfrow)
}
par(#mfrow=compProps$mfrow,
oma=compProps$oma,
xpd=compProps$xpd,
bg=compProps$bg,
mar = if(is.null(margins) ){ c(2.6*(1+(compProps$cx-1)/2),4.1*(1+(compProps$cx-1)/4),4.1,2.1)}else{margins})
# layout(t(as.matrix(c(1,2))))
for(plotgroup in c(1:length(grouping))){
#par(mfrow=c(1,2))
items = grouping[[plotgroup]]
preminoritem <- if(nrowcheck ==1){EIClist}else{EIClist[majoritem,]}
minoritem <- subsetEICs(preminoritem,
items)
#minoritem <- if(length(items) == 1){t(as.matrix(EIClist[[majoritem]][items,]))}else{EIClist[[majoritem]][items,]}
#if(length(items) == 1){row.names(minoritem) <- items}
xlimes = if (is.null(plotProps$xlim)){c(min(unlist(minoritem$EIClist[[1]][,'rt'])),
max(unlist(minoritem$EIClist[[1]][,'rt'])))/60}
else{c(min(plotProps$xlim[majoritem,]), max(plotProps$xlim[majoritem,]))/60}
### by default, only the visible part of the spectrum will be used to determine y-max
if(!is.null(plotProps$ylim) && !names(grouping)[plotgroup] %in% RescaleExclude){
ylimes = c(0,1)
try({
ylimes = c(min(plotProps$ylim[majoritem,]), max(plotProps$ylim[majoritem,]))
})
}else if(plotProps$TIC){
mm <- 1
for(k in 1:length(minoritem$EIClist)){
mm <- max(mm,
suppressWarnings({
max(unlist(minoritem$EIClist[[k]][,"tic"])[which(unlist(minoritem$EIClist[[k]][,"rt"]) >= min(xlimes)*60
& unlist(minoritem$EIClist[[k]][,"rt"]) <= max(xlimes)*60)])
}) #warnings occur if all scans are out of given rt range
)
}
ylimes = c(0,mm)
}
else{
mm <- 1
for(k in 1:length(minoritem$EIClist)){
mm <- max(mm,
suppressWarnings({
max(unlist(minoritem$EIClist[[k]][,"intensity"])[which(unlist(minoritem$EIClist[[k]][,"rt"]) >= min(xlimes)*60
& unlist(minoritem$EIClist[[k]][,"rt"]) <= max(xlimes)*60)])
}) #warnings occur if all scans are out of given rt range
)
}
ylimes = c(0,mm)
}
if(raise){ylimes[1] <- -0.02*max(ylimes)}
EICplot(EICs = minoritem$EIClist, cx = plotProps$cx,
ylim = ylimes,
xlim = xlimes,
colr = if(is.list(plotProps$colr)){plotProps$colr[[plotgroup]]$color}
else{plotProps$colr[1:nrow(minoritem$EIClist[[1]])]},
legendtext = if(is.list(plotProps$colr)){plotProps$colr[[plotgroup]]}
else{paste(sub("^([^.]*).*", "\\1",basename(row.names(minoritem$EIClist[[1]]))))},
heading = names(grouping)[plotgroup],
relto = if(relPlot){max(ylimes)}else{NULL},
TIC = plotProps$TIC,
lw = plotProps$lw,
midline = plotProps$midline[majoritem],
yzoom = plotProps$yzoom,
ylabshift = ylabshift
#mfrow=c(1,2)
)
# }
}
if(!is.null(compProps$header)){
title(main = compProps$header[majoritem], outer=T,line=2, cex.main=autosize, font = 2)}
if(!is.null(compProps$header2)){mtext(compProps$header2[majoritem], side=3, outer=T,line=0, cex=compProps$cx)}
}
if(!is.null(compProps$pdfFile)){dev.off()}
}
#' EICplot
#'
#' generate one EIC plot for multiple files in one plot window.
#'
#' @return sends a single EIC plot to the current plotting device
#'
#' @param EICs item from a list of EICs from Metaboseek:multiEIC
#' @param cx character expansion (font size) factor
#' @param ylim numeric(2) min and max visible rt value (in seconds)
#' @param xlim numeric(2) min and max visible intensity value (in seconds)
#' @param legendtext character() with item for each shown EIC for the plot legend
#' @param colr color range (actual vector of color values)
#' @param heading plot title
#' @param relto normalize intensities to this number
#' @param TIC if TRUE plot TIC
#' @param single TRUE if this is not part of a composite plot
#' @param midline numeric() of y-axis positions where a dotted vertical line should be plotted
#' @param lw line width for plot lines
#' @param yzoom zoom factor into y-axis
#' @param ylabshift shift horizontal position of y axis label
#'
#' @export
EICplot <- function(EICs, cx = 1,
ylim = c(0,max(unlist(EICs[[1]][,'tic']))),
xlim = c(min(unlist(EICs[[1]][,'rt'])),
max(unlist(EICs[[1]][,'rt'])))/60,
legendtext = paste(sub("^([^.]*).*", "\\1",basename(row.names(EICs[[1]])))),
colr = topo.colors(nrow(EICs[[1]]), alpha=1),
heading = "test",
relto = NULL,
TIC = F,
single = F,
midline = 100,
lw = 1,
yzoom = 1,
ylabshift = 0
){
suppressWarnings({
if(max(ylim)==0
|| !is.finite(max(ylim))){ylim = c(0,1)}
})
maxint <- format(max(ylim), digits =3, scientific = T)
if(!is.null(relto) && relto != 1 ){
maxint <- format(relto, digits =3, scientific = T)
}
if(is.null(relto)){relto <-1}
if(!is.null(yzoom) && yzoom != 1 ){
ylim[2] <- ylim[2]/yzoom
}
if(!is.null(relto) && relto != 1 ){ylim <- (ylim/relto)*100}
PlotWindow(cx,
ylim,
xlim,
heading,
single,
ysci = if(!is.null(relto) && relto != 1){F}else{T},
liwi = lw,
ylab = if(!is.null(relto) && relto != 1){"Relative Intensity (%)"}else{"Intensity"},
ylabshift = ylabshift
)
if(length(midline)> 0 ){
for(i in midline){
abline(v=i/60, lty = 2, lwd = 1)
}
}
##draw the eics
addLines(EIClist = EICs,
TIC,
colr,
relto = relto,
liwi = lw
)
#fix axis to not have gaps at edges
abline(v=min(xlim), h=min(ylim))
par(xpd=NA)
text(min(xlim), max(ylim)+1.5*strheight("M"),
labels = maxint, bty="n",
font = 2, cex=cx*1)
if(!is.null(legendtext)){
if(is.list(legendtext)){
legendtext <- legendtext[!duplicated(legendtext),]
legend("topright",
# inset=c(-0.08,-0.08),#c(0.025*max(xlim),0.025*max(ylim)),
legend = legendtext$label, lty=1,lwd=2.5, col=legendtext$color, bty="n", cex=cx*0.7)
}else{
legend("topright",
# inset=c(-0.08,-0.08),#c(0.025*max(xlim),0.025*max(ylim)),
legend = legendtext, lty=1,lwd=2.5, col=colr, bty="n", cex=cx*0.7)
}
}
}
#' addLines
#'
#' Helper function for EICplot to plot the lines of EICs into a PlottingWindow.
#' Mass shifts will be handled by plotting different line types
#'
#' @return plots EIC trace lines into the current plot window
#'
#' @param EIClist matrix or list of EIC objects (potentially subsetted)
#' @param TIC logical() if TRUE, TIC will be plotted instead of EIC
#' @param colr character() of color values for lines
#' @param relto if not NULL, intensities will be given as relative to this numeric(1)
#' @param liwi line width of plotted lines
#'
addLines <- function(EIClist,
TIC = F,
colr = topo.colors(1, alpha=1),
relto = NULL,
liwi = 2
){
if(TIC){
reps <- 1
}else{
reps <- length(EIClist)
}
for(n in 1:reps){
if(TIC){
int <- EIClist[[n]][,'tic']
}else{
int <- EIClist[[n]][,'intensity']
}
if(!is.null(relto) && relto != 1 ){
int <- lapply(lapply(int,"/",relto),"*",100)
# maxint <- format(relto, digits =3, scientific = T)
}
#convert to minutes
rts <- lapply(EIClist[[n]][,"rt"],"/",60)
# par(xpd=NA)
# options(scipen=20)
#colr <- topo.colors(2, alpha=1)#rainbow(length(eiccoll[[t]]), s = 1, v = 1, start = 0, end = max(1, length(eiccoll[[t]]) - 1)/length(eiccoll[[t]]), alpha = 0.7)#topo.colors(length(eiccoll[[t]]), alpha=1)
##draw the eics
tmp <-mapply(lines, x= rts, y = int, col = as.list(colr), MoreArgs = list(lty = n, lwd = liwi))}
}
#' legendplot
#'
#' Plot a legend in an otherwise empty plot
#'
#' @param ... all arguments passed on to \code{\link[graphics]{legend}()}
#'
#' @return calls a new \code{plot()} with a legend
#'
legendplot <- function(...){
par(mfrow=c(1,1),
mar = c(0.1,0.1,0.1,0.1),
oma = c(0,0,0,0)
)
plot(1, type = "n", axes=FALSE, xlab="", ylab="")
legend(...)
}
mjhelf/Metaboseek documentation built on April 23, 2022, 12:09 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions legendplot addLines EICplot groupPlot EICtitles EICgeneral
Documented in addLines EICgeneral EICplot EICtitles groupPlot legendplot
#' EICgeneral
#'
#' wrapper function to plot multiple EICs
#'
#'
#' @param rtmid vector of retention time values (not ranges). If length >1,
#' multiple plots are called (multiple pages in pdf file)
#' @param mzmid vector of mz values (not ranges).
#' Has to be same length as \code{rtmid}
#' @param glist a named list of grouped file names
#' (as supplied in $grouping of rawLayout objects)
#' @param cols integer, number of columns in plot. if NULL,
#' grid can be defined externally
#' @param colrange character(1), color range function used for line colors,
#' OR a list of data.frames, see \code{Details}
#' @param transparency numeric(1), alpha (range 0..1) for transparency of lines
#' @param RTall if TRUE, entire RT range will be plotted
#' @param TICall if TRUE, TIC will be plotted instead of EIC
#' @param rtw retention time window +/- rtmid in seconds that will be plotted
#' @param ppm mz window +/- mzmid in ppm that will be plotted
#' @param rdata named list of xcmsRaw objects
#' @param pdfFile character - if not NULL, plotting result will be saved in a
#' pdf file with this name.
#' @param leadingTIC if TRUE, a TIC plot is made before the EIC plots
#' (e.g. as first page of pdf file)
#' @param midline if TRUE, dotted vertical line should be plotted at feature rt
#' @param lw line width for plot lines
#' @param yzoom zoom factor into y-axis
#' @param cx character expansion factor (font size)
#' @param adducts numeric() of mass shifts to be added to feature masses
#' @param RTcorrect if not NULL, this RTcorr object will be used to
#' adjust retention times.
#' @param importEIC a \code{\link{multiEICplus}()} output object to plot here, If NULL,
#' \code{multiEICplus()} is called with the other supplied parameters
#' @param globalYmax if TRUE, all EICs are scaled to the maximum value across all
#' plotting groups instead of the maximum within each group
#' @param subtitles subtitles for each EIC, must be character of
#' same length as rtmid and mzmid or NULL
#' @param raise if TRUE, EIC will be plotted with y axis going to
#' -0.02*max(ylim) so that EICs with 0 intensity are visible.
#' @param relPlot if TRUE, y-axis will show relative intensities
#' @param margins manual setting for plot margins (par$mar)
#' @param ylabshift shift horizontal position of y axis label
#' @param RescaleExclude character(), exclude this group from rescaling, or NULL to use all
#'
#' @return sends a grouped EIC plot to the current plotting device, or
#' generates a .pdf file
#'
#' @details
#' \describe{
#' \item{colrange}{A named list with the same structure as \code{glist},
#' but with a data.frame in each list element with row order corresponding to
#' items in the list elements of \code{glist} and columns \code{color} and \code{label},
#' specifying the EIC color and legend label for each EIC trace.
#' }
#' }
#'
#' @export
EICgeneral <- function(rtmid,
mzmid,
glist,
cols = NULL,
colrange = "Mseek.colors",
transparency = 1,
RTall = FALSE,
TICall = FALSE,
rtw = 30,
ppm = 5,
rdata,
pdfFile = "plotOutput.pdf",
leadingTIC = T,
lw = 1,
adducts = c(0),
cx = 1,
midline = T,
yzoom = 1,
RTcorrect = NULL,
importEIC = NULL,
globalYmax = FALSE,
subtitles = NULL,
raise = F,
relPlot = F,
margins = NULL,
ylabshift = 0,
RescaleExclude = NULL
){
#number of plot rows
if(!is.null(cols)){
rows <- ceiling(length(glist)/cols)
}else{
rows <-1}
if(!is.list(colrange)){
#make color scales for each group, color shades based on group with most members
colvec <- do.call(colrange,
list(n=max(sapply(glist,length)), alpha = transparency))
colrs <- list()
for(i in 1:length(glist)){
colrs[[i]] <- data.frame(color = colvec[1:length(glist[[i]])],
label = sub("^([^.]*).*", "\\1",basename(glist[[i]])),
stringsAsFactors = FALSE)
}}
else{
colrs <- colrange
}
# print(colrs)
#generate rt boundary df
if(any(RTall, is.null(rtmid))){ # any can handle NULL, seems more flexible than ||
rtmid <- NULL
rtx <- NULL
}else{
rtx <- data.frame(rtmin = rtmid - rtw,
rtmax = rtmid + rtw)
}
#generate mz boundary df
if(any(TICall, is.null(mzmid)) ){
mzmid <- if(!is.null(rtmid)){rep(100,length(rtmid))}else{100}
mzx <- data.frame(mzmin = mzmid-1,
mzmax = mzmid+1)
titx <- if(!is.null(rtmid)){rep("TICs",length(rtmid))}else{"TICs"}
tictog <- TRUE
}else{
tictog <- FALSE
mzx <- data.frame(mzmin = mzmid - mzmid*ppm*1e-6,
mzmax = mzmid + mzmid*ppm*1e-6)
titx <- EICtitles(mzmid, rtmid, ppm)
}
if(length(titx) != length(subtitles)){ subtitles <-NULL}
#optionally export to pdf
if(!is.null(pdfFile)){
if(is.null(cols)){
rows <- ceiling(length(glist)/5)
cols <-1}
pdf(pdfFile,
6*cols,
6*ceiling(length(glist)/cols)+2
)}
#optionally plot TICs first (page 1 in pdf)
if(leadingTIC){
EICsTIC <- multiEIC(rawdata= rdata[basename(names(rdata)) %in% basename(unlist(glist))],
mz = mzx[1,],
rt = NULL,
rnames = "1", #major item names
byFile = F,#if true, table will be sorted by rawfile, otherwise by feature
RTcorr = RTcorrect
)
yl <- if(!is.null(globalYmax)
&& globalYmax){matrix(c(rep(0, length(EICsTIC)),
sapply(EICsTIC, function(x){ max(unlist(x[,"tic"])) })), ncol = 2, byrow = F)}else{NULL}
groupPlot(EIClist = EICsTIC,
grouping = glist,
plotProps = list(TIC = T, #settings for single plots
cx = cx,
colr = colrs,
lw = lw,
midline = NULL,
ylim = yl, #these should be data.frames or matrices of nrow = number of plotted features
xlim = NULL,
yzoom = 1),
compProps = list(mfrow=c(rows,cols), #par options for the composite plot
oma=c(0,2,4,0),
xpd=NA, bg="white",
header = "TICs",
header2 = NULL,
pdfFile = NULL,
pdfHi = 6*rows,
pdfWi = 6*cols,
cx = cx,
adductLabs = 0),
raise,
relPlot,
margins,
ylabshift
)
}
if(is.null(importEIC)){
EICs <- multiEICplus(rawdata= rdata[basename(names(rdata)) %in% basename(unlist(glist))],
mz = mzx,
rt = if(is.null(RTcorrect)){rtx}else{NULL},
rnames = row.names(mzmid), #major item names
byFile = F, #if true, table will be sorted by rawfile, otherwise by feature
adducts,
RTcorr = RTcorrect
)}
else{
EICs <- importEIC
}
if(!is.null(RescaleExclude)
&& length(na.omit(match(RescaleExclude,names(glist)))) > 0
&& length(na.omit(match(RescaleExclude,names(glist)))) < length(glist)){
excludedfiles <- unlist(glist[match(RescaleExclude,names(glist))])
}else{
excludedfiles <- character(0)
}
if(TICall){
if(is.null(rtx) || length(EICs) %% nrow(rtx) != 0 ){
yl <- if(!is.null(globalYmax)
&& globalYmax){matrix(c(rep(0, length(EICs)),
sapply(EICs, function(x){ max(unlist(x[,"tic"])) })), ncol = 2, byrow = F)}else{NULL}
}
else{
suppressWarnings({
yl <- if(!is.null(globalYmax)
&& globalYmax){matrix(c(rep(0, length(EICs)),
mapply(function(x, rt){ max(unlist(x[,"tic"])[unlist(x[,"rt"]) >= max(c(min(rt),min(unlist(x[,"rt"])))) & unlist(x[,"rt"]) <= min(c(max(rt),max(unlist(x[,"rt"]))))])}, x = EICs, rt = as.list(as.data.frame(t(as.matrix(rtx)))) )), ncol = 2, byrow = F)}else{NULL}
}) #warnings occur if all scans are out of given rt range
}
}else{
#make sure the EICs all get scaled to their highest intensity across all adducts
if(is.null(rtx) || length(EICs) %% nrow(rtx) != 0 ){
maxys <- Biobase::rowMax(matrix(sapply(EICs, function(x){ max(unlist(x[which(!rownames(x) %in% excludedfiles),"intensity"])) }), ncol = length(adducts), byrow = F))
}else{
suppressWarnings({
maxys <- Biobase::rowMax(matrix(mapply(function(x, rt){
subsel <- which(!rownames(x) %in% excludedfiles)
max(unlist(x[subsel,"intensity"])[unlist(x[subsel,"rt"]) >= max(c(min(rt),min(unlist(x[subsel,"rt"]))))
& unlist(x[subsel,"rt"]) <= min(c(max(rt),max(unlist(x[subsel,"rt"]))))])},
x = EICs, rt = as.list(as.data.frame(t(as.matrix(rtx)))) ), ncol = length(adducts), byrow = F))
}) #warnings occur if all scans are out of given rt range
}
yl <- if(!is.null(globalYmax) && globalYmax){matrix(c(rep(0, length(EICs)),rep(maxys, length(adducts))), ncol = 2, byrow = F)}else{NULL}
}
groupPlot(EIClist = EICs,
grouping = glist,
plotProps = list(TIC = tictog, #settings for single plots
cx = cx,
colr = colrs,
xlim = rtx,
ylim = yl, #these should be data.frames or matrices of nrow = number of plotted features
lw = lw,
midline = if(midline){rtmid}else{NULL},
yzoom = yzoom),
compProps = list(mfrow=c(rows,cols), #par options for the composite plot
oma=c(0,2,4,0),
xpd=NA, bg="white",
header = titx,
header2 = subtitles,
pdfFile = NULL,
pdfHi = 6*rows,
pdfWi = 6*cols,
cx = cx,
adductLabs = adducts),
raise,
relPlot,
margins,
ylabshift,
RescaleExclude
)
if(!is.null(pdfFile)){dev.off()}
}
#' EICtitles
#'
#' helper function to generate titles for EICgeneral
#'
#'
#' @param rts vector of retention time values (not ranges)
#' @param mzs vector of mz values (not ranges)
#' @param ppm mz window +/- mzmid in ppm that will be plotted
#'
#' @return a character vector with plot titles of same length as
#' \code{rts} and \code{mzs}
#'
EICtitles <- function(mzs, rts, ppm){
if(!is.null(ppm)){
numbs <- matrix(mapply(sprintf,matrix(c(mzs,
mzs-mzs*ppm*1e-6,
mzs+mzs*ppm*1e-6),ncol=3),
MoreArgs = list(fmt = "%.5f")),
ncol=3)
titx <- paste0('m/z range: ',numbs[,1], " +/- ",
format(ppm, scientific = F),
" ppm (", numbs[,2]," - ", numbs[,3],")",
if(!is.null(rts)){
paste0(
" @ RT: ", sprintf( "%.2f", rts/60), " min",
" (", sprintf("%.1f", rts)," sec)")})
}
else{
numbs <- sprintf("%.5f", mzs)
titx <- paste0('m/z: ',numbs,
if(!is.null(rts)){
paste0(
" @ RT: ", sprintf( "%.2f", rts/60), " min",
" (", sprintf("%.1f", rts)," sec)")})
}
return(titx)
}
#' groupPlot
#'
#' generate multiple EICs on one page
#'
#'
#' @param EIClist list of EICs from \code{\link{multiEIC}()} or \code{\link{multiEICplus}()}
#' @param grouping a named list of grouped file names (as supplied in $grouping of rawLayout objects)
#' @param plotProps a list of settings for the individual plots, see \code{Details}
#' @param compProps layoout options for the composite plot, see \code{Details}
#' @param raise if TRUE, EIC will be plotted with y axis going to -0.02*max(ylim) so that EICs with 0 intensity are visible.
#' @param relPlot if TRUE, y-axis will show relative intensities
#' @param margins manual setting for plot margins (par$mar)
#' @param ylabshift shift horizontal position of y axis label
#' @param RescaleExclude character(), exclude this group from rescaling, or NULL to use all
#'
#' @return sends a grouped EIC plot to the current plotting device
#'
#' @details
#' \describe{
#' \item{plotProps}{A list with these elements:
#' \itemize{
#' \item \code{TIC} if TRUE, TIC instead of EIC
#' \item \code{cx} numeric(1) font size (character expansion) factor
#' \item \code{colr} color range (actual vector of color values)
#' \item \code{ylim} data.frame or matrix of nrow = number of plotted features,
#' with min and max visible rt value (in seconds) for each feature
#' \item \code{xlim} data.frame or matrix of nrow = number of plotted features,
#' with min and max visible intensity value for each feature
#' \item \code{midline} numeric() of y-axis positions where a dotted vertical
#' line should be plotted
#' \item \code{lw} line width for plot lines
#' \item \code{yzoom} zoom factor into y-axis
#' }
#' }
#' \item{compProps}{
#' \itemize{
#' \item \code{mfrow} integer(2) rows and columns for plotting (cf. par(), mfrow)
#' \item \code{oma} numeric(4) outer margins (cf. par(), oma)
#' \item \code{xpd} drawing outside of plot region, cf. par(), xpd
#' \item \code{bg} background color, cf. par(), bg
#' \item \code{header} First (title) line of composite plot
#' \item \code{header2} Subtitle line of composite plot
#' \item \code{pdfFile} character - if not NULL, plotting result will be saved in a pdf file with this name.
#' \item \code{pdfHi} pdf height in inches
#' \item \code{pdfWi} pdf width in inches
#' \item \code{cx} numeric(1) font size (character expansion) factor
#' \item \code{adductLabs} adduct labels (nonfunctional)
#' }
#' }
#' }
#'
#' @export
groupPlot <- function(EIClist,
grouping,
plotProps = list(TIC = TRUE, #settings for single plots
cx = 1,
colr = topo.colors(nrow(EIClist[[1]]), alpha=1),
ylim = NULL, #these should be data.frames or matrices of nrow = number of plotted features
xlim = NULL,
lw = 1,
midline = 100,
yzoom = 1),
compProps = list(mfrow=c(1,2), #par options for the composite plot
oma=c(0,2,8,0),
xpd=NA, bg=NA,
header = paste0(names(EIClist)),
header2 = NULL,
pdfFile = NULL,
pdfHi = 6,
pdfWi = 12,
cx = 1,
adductLabs = c("0","1","2")),
raise = F,
relPlot = F,
margins = NULL,
ylabshift = 0,
RescaleExclude = NULL
){
#majoritem is the EIClist top level (typically by mz, but could be)
if(!is.null(compProps$pdfFile)){pdf(compProps$pdfFile,compProps$pdfWi,compProps$pdfHi)}
if(!is.null(compProps$header)){
autosize <- compProps$cx*1.5
while(max(strwidth(compProps$header, units = "figure", cex = autosize, font = 2)) > 1){
autosize <- autosize*0.975
}
}
nrowcheck <- if(!is.null(nrow(EIClist))){nrow(EIClist)}else {1}
for(majoritem in c(1:nrowcheck)){
#adductLabs legend does not work yet
#if(length(compProps$adductLabs)>1){compProps$mfrow[1] <- compProps$mfrow[1]+1}
if(length(compProps$mfrow) > 1){
par(mfrow=compProps$mfrow)
}
par(#mfrow=compProps$mfrow,
oma=compProps$oma,
xpd=compProps$xpd,
bg=compProps$bg,
mar = if(is.null(margins) ){ c(2.6*(1+(compProps$cx-1)/2),4.1*(1+(compProps$cx-1)/4),4.1,2.1)}else{margins})
# layout(t(as.matrix(c(1,2))))
for(plotgroup in c(1:length(grouping))){
#par(mfrow=c(1,2))
items = grouping[[plotgroup]]
preminoritem <- if(nrowcheck ==1){EIClist}else{EIClist[majoritem,]}
minoritem <- subsetEICs(preminoritem,
items)
#minoritem <- if(length(items) == 1){t(as.matrix(EIClist[[majoritem]][items,]))}else{EIClist[[majoritem]][items,]}
#if(length(items) == 1){row.names(minoritem) <- items}
xlimes = if (is.null(plotProps$xlim)){c(min(unlist(minoritem$EIClist[[1]][,'rt'])),
max(unlist(minoritem$EIClist[[1]][,'rt'])))/60}
else{c(min(plotProps$xlim[majoritem,]), max(plotProps$xlim[majoritem,]))/60}
### by default, only the visible part of the spectrum will be used to determine y-max
if(!is.null(plotProps$ylim) && !names(grouping)[plotgroup] %in% RescaleExclude){
ylimes = c(0,1)
try({
ylimes = c(min(plotProps$ylim[majoritem,]), max(plotProps$ylim[majoritem,]))
})
}else if(plotProps$TIC){
mm <- 1
for(k in 1:length(minoritem$EIClist)){
mm <- max(mm,
suppressWarnings({
max(unlist(minoritem$EIClist[[k]][,"tic"])[which(unlist(minoritem$EIClist[[k]][,"rt"]) >= min(xlimes)*60
& unlist(minoritem$EIClist[[k]][,"rt"]) <= max(xlimes)*60)])
}) #warnings occur if all scans are out of given rt range
)
}
ylimes = c(0,mm)
}
else{
mm <- 1
for(k in 1:length(minoritem$EIClist)){
mm <- max(mm,
suppressWarnings({
max(unlist(minoritem$EIClist[[k]][,"intensity"])[which(unlist(minoritem$EIClist[[k]][,"rt"]) >= min(xlimes)*60
& unlist(minoritem$EIClist[[k]][,"rt"]) <= max(xlimes)*60)])
}) #warnings occur if all scans are out of given rt range
)
}
ylimes = c(0,mm)
}
if(raise){ylimes[1] <- -0.02*max(ylimes)}
EICplot(EICs = minoritem$EIClist, cx = plotProps$cx,
ylim = ylimes,
xlim = xlimes,
colr = if(is.list(plotProps$colr)){plotProps$colr[[plotgroup]]$color}
else{plotProps$colr[1:nrow(minoritem$EIClist[[1]])]},
legendtext = if(is.list(plotProps$colr)){plotProps$colr[[plotgroup]]}
else{paste(sub("^([^.]*).*", "\\1",basename(row.names(minoritem$EIClist[[1]]))))},
heading = names(grouping)[plotgroup],
relto = if(relPlot){max(ylimes)}else{NULL},
TIC = plotProps$TIC,
lw = plotProps$lw,
midline = plotProps$midline[majoritem],
yzoom = plotProps$yzoom,
ylabshift = ylabshift
#mfrow=c(1,2)
)
# }
}
if(!is.null(compProps$header)){
title(main = compProps$header[majoritem], outer=T,line=2, cex.main=autosize, font = 2)}
if(!is.null(compProps$header2)){mtext(compProps$header2[majoritem], side=3, outer=T,line=0, cex=compProps$cx)}
}
if(!is.null(compProps$pdfFile)){dev.off()}
}
#' EICplot
#'
#' generate one EIC plot for multiple files in one plot window.
#'
#' @return sends a single EIC plot to the current plotting device
#'
#' @param EICs item from a list of EICs from Metaboseek:multiEIC
#' @param cx character expansion (font size) factor
#' @param ylim numeric(2) min and max visible rt value (in seconds)
#' @param xlim numeric(2) min and max visible intensity value (in seconds)
#' @param legendtext character() with item for each shown EIC for the plot legend
#' @param colr color range (actual vector of color values)
#' @param heading plot title
#' @param relto normalize intensities to this number
#' @param TIC if TRUE plot TIC
#' @param single TRUE if this is not part of a composite plot
#' @param midline numeric() of y-axis positions where a dotted vertical line should be plotted
#' @param lw line width for plot lines
#' @param yzoom zoom factor into y-axis
#' @param ylabshift shift horizontal position of y axis label
#'
#' @export
EICplot <- function(EICs, cx = 1,
ylim = c(0,max(unlist(EICs[[1]][,'tic']))),
xlim = c(min(unlist(EICs[[1]][,'rt'])),
max(unlist(EICs[[1]][,'rt'])))/60,
legendtext = paste(sub("^([^.]*).*", "\\1",basename(row.names(EICs[[1]])))),
colr = topo.colors(nrow(EICs[[1]]), alpha=1),
heading = "test",
relto = NULL,
TIC = F,
single = F,
midline = 100,
lw = 1,
yzoom = 1,
ylabshift = 0
){
suppressWarnings({
if(max(ylim)==0
|| !is.finite(max(ylim))){ylim = c(0,1)}
})
maxint <- format(max(ylim), digits =3, scientific = T)
if(!is.null(relto) && relto != 1 ){
maxint <- format(relto, digits =3, scientific = T)
}
if(is.null(relto)){relto <-1}
if(!is.null(yzoom) && yzoom != 1 ){
ylim[2] <- ylim[2]/yzoom
}
if(!is.null(relto) && relto != 1 ){ylim <- (ylim/relto)*100}
PlotWindow(cx,
ylim,
xlim,
heading,
single,
ysci = if(!is.null(relto) && relto != 1){F}else{T},
liwi = lw,
ylab = if(!is.null(relto) && relto != 1){"Relative Intensity (%)"}else{"Intensity"},
ylabshift = ylabshift
)
if(length(midline)> 0 ){
for(i in midline){
abline(v=i/60, lty = 2, lwd = 1)
}
}
##draw the eics
addLines(EIClist = EICs,
TIC,
colr,
relto = relto,
liwi = lw
)
#fix axis to not have gaps at edges
abline(v=min(xlim), h=min(ylim))
par(xpd=NA)
text(min(xlim), max(ylim)+1.5*strheight("M"),
labels = maxint, bty="n",
font = 2, cex=cx*1)
if(!is.null(legendtext)){
if(is.list(legendtext)){
legendtext <- legendtext[!duplicated(legendtext),]
legend("topright",
# inset=c(-0.08,-0.08),#c(0.025*max(xlim),0.025*max(ylim)),
legend = legendtext$label, lty=1,lwd=2.5, col=legendtext$color, bty="n", cex=cx*0.7)
}else{
legend("topright",
# inset=c(-0.08,-0.08),#c(0.025*max(xlim),0.025*max(ylim)),
legend = legendtext, lty=1,lwd=2.5, col=colr, bty="n", cex=cx*0.7)
}
}
}
#' addLines
#'
#' Helper function for EICplot to plot the lines of EICs into a PlottingWindow.
#' Mass shifts will be handled by plotting different line types
#'
#' @return plots EIC trace lines into the current plot window
#'
#' @param EIClist matrix or list of EIC objects (potentially subsetted)
#' @param TIC logical() if TRUE, TIC will be plotted instead of EIC
#' @param colr character() of color values for lines
#' @param relto if not NULL, intensities will be given as relative to this numeric(1)
#' @param liwi line width of plotted lines
#'
addLines <- function(EIClist,
TIC = F,
colr = topo.colors(1, alpha=1),
relto = NULL,
liwi = 2
){
if(TIC){
reps <- 1
}else{
reps <- length(EIClist)
}
for(n in 1:reps){
if(TIC){
int <- EIClist[[n]][,'tic']
}else{
int <- EIClist[[n]][,'intensity']
}
if(!is.null(relto) && relto != 1 ){
int <- lapply(lapply(int,"/",relto),"*",100)
# maxint <- format(relto, digits =3, scientific = T)
}
#convert to minutes
rts <- lapply(EIClist[[n]][,"rt"],"/",60)
# par(xpd=NA)
# options(scipen=20)
#colr <- topo.colors(2, alpha=1)#rainbow(length(eiccoll[[t]]), s = 1, v = 1, start = 0, end = max(1, length(eiccoll[[t]]) - 1)/length(eiccoll[[t]]), alpha = 0.7)#topo.colors(length(eiccoll[[t]]), alpha=1)
##draw the eics
tmp <-mapply(lines, x= rts, y = int, col = as.list(colr), MoreArgs = list(lty = n, lwd = liwi))}
}
#' legendplot
#'
#' Plot a legend in an otherwise empty plot
#'
#' @param ... all arguments passed on to \code{\link[graphics]{legend}()}
#'
#' @return calls a new \code{plot()} with a legend
#'
legendplot <- function(...){
par(mfrow=c(1,1),
mar = c(0.1,0.1,0.1,0.1),
oma = c(0,0,0,0)
)
plot(1, type = "n", axes=FALSE, xlab="", ylab="")
legend(...)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.