R/Function_specplot.R
In mjhelf/METABOseek: Metaboseek platform
Defines functions
parseTitle
Documented in
parseTitle
#' parseTitle
#'
#' parse a scanInfo table into a title for a mass spectrum plot
#'
#' @return a character vector of length 1.
#'
#' @param scanInfo a data.frame as returned by \link{getScanInfo}()
#'
#' @export
parseTitle <- function(scanInfo){
if(is.null(scanInfo) ||nrow(scanInfo) == 0){
return("")
}
if(nrow(scanInfo) ==1){
return(
paste0(basename(scanInfo$filename), "#",
scanInfo$acquisitionNum,
" (", round(scanInfo$retentionTime/60,3), " min)",
if(scanInfo$precursorMZ != 0){
paste0("\nParent m/z: ",
format(round(scanInfo$precursorMZ,5),
nsmall = 5, scientific = F))}else{""},
collapse = " ")
)
}
if(all(scanInfo$msLevel == scanInfo$msLevel[1])){
return(
paste0(
if(length(unique(scanInfo$filename)) == 1){
paste0(scanInfo$filename[1],"#",
min(scanInfo$acquisitionNum),"-",
max(scanInfo$acquisitionNum),
"[",nrow(scanInfo)," scans]")
}else{
paste0("[",length(unique(scanInfo$filename)),
" files][",nrow(scanInfo)," scans]")
},
"(",
round(min(scanInfo$retentionTime)/60,3),
" - ",
round(max(scanInfo$retentionTime)/60,3),
" min)",
if(scanInfo$msLevel[1] > 1){
paste0("\nParent m/z: ",
round(mean(scanInfo$precursorMZ),5))}else{""}
)
)
}
return("Mixed different MS levels")
}
#' specplot2
#'
#' Plot an MS spectrum
#'
#' @param x mz coordinates
#' @param y intensity coordinates
#' @param spectrum matrix or data.frame, where the first column is m/z values,
#' and the second column are intensity values
#' @param norm normalize by
#' @param cx font size
#' @param k top k intensity peaks will be labeled
#' automatically with their mz values
#' @param fileName plot title
#' @param yrange y axis range
#' @param xrange x axis range
#' @param maxi max intensity to be plotted on side.
#' @param labels data.frame containing at least x and y coordinates,
#' plus optional columns: label and color
#' @param highlights matrix or data.frame, see \code{details}
#' @param mar margins passed to par()
#' @param ylab y axis label
#' @param ylabshift shift horizontal position of y axis label
#' @param parseLabels if TRUE, the \code{label} column in \code{labels} will
#' be parsed (using \code{\link[base]{parse}})
#'
#' @details
#' \describe{
#' \item{highlights}{matrix or data.frame with at the first two columns
#' containing x and y coordinates of peaks to highlight.
#' If \code{highlights} has an additional column called \code{color},
#' that column is expected to contain color values for the highlights.
#' If \code{highlights} has an additional column called \code{type},
#' that column is expected to contain point \code{type} values for the highlights,
#' as detailed in \link[graphics]{plot.default}.}
#' \item{labels}{
#' The first two columns of this data.frame will be assumed to be mz and intensity values, respectively.
#' If it only contains two columns, the first column values will be used as label text.
#' If a \code{label} column is present, that column will be used as peak labels.
#' If a \code{colors} column is present, that column will be used to define
#' the label color, otherwise it will be red.
#' }
#' \item{parseLabels}{
#' Parsing labels can be used to include subscript and
#' superscript elements in peak labels, but requires careful preparation
#' of the strings to be passed to \code{\link[base]{parse}}
#' }
#' }
#'
#' @return plots a spectrum view in the current plotting device
#'
#' @importFrom TeachingDemos spread.labs
#' @importFrom Hmisc minor.tick
#' @export
specplot2 <- function (x,
y,
spectrum,
norm= NULL,
cx=1,
k = 10,
fileName = "",
yrange = NULL,
xrange = NULL,
maxi = NULL,
labels = NULL,
highlights = NULL,
mar = c(3,4,6,1),
ylab = "Relative Intensity (%)",
ylabshift = 2,
parseLabels = F
){
if(!missing(spectrum) && !is.null(spectrum)){
if(is.null(xrange)){
xrange <- range(spectrum[,1])
sel <- TRUE
}else{
sel <- spectrum[,1] <= max(xrange) & spectrum[,1] >= min(xrange)
}
if(nrow(spectrum) == 0){
maxi <- 100
norm <- 1
}else{
#by default, scale largest y value in view to 100,
#to scale globally, set maxi to max(y) externally
if(is.null(maxi)){maxi <- if(!any(sel)
|| length(sel) == 0){100}else{max(spectrum[sel,2, drop = F])}}
if(!any(sel) || length(sel) == 0 || maxi == 0){
norm = 1
}
if(is.null(norm)){
norm = maxi/100
}
spectrum <- spectrum[sel,, drop = F]
}
spectrum[,2] <- spectrum[,2]/norm
}else{
if(is.null(xrange)){xrange = range(x)}
sel <- x <= max(xrange) & x >= min(xrange)
#by default, scale largest y value in view to 100,
#to scale globally, set maxi to max(y) externally
if(is.null(maxi)){maxi <- if(length(sel) == 0){1}else{max(y[sel])}}
if(length(sel) == 0 || maxi == 0){
norm = 1
}
if(is.null(norm)){
norm = maxi/100
}
spectrum <- data.frame(x=x[sel],
y=y[sel]/norm)
}
if(is.null(yrange)){yrange = c(0, maxi/norm)}
par(#oma=c(0,2,0,0), #oma causes issues with selectcallback
mar = mar,
xpd = FALSE, xaxs = "i", yaxs = "i")
PlotWindow(cx,
ylim = yrange,
xlim = xrange,
heading = fileName,
single = T,
par = F,
relto = norm,
ylab,
xlab = "m/z",
ysci = F,
textadj = 1,
ylabshift = ylabshift
)
if(!is.null(highlights)){
highlights[,2] <- highlights[,2]/norm
points(highlights[,1],highlights[,2],
type= if("type" %in% colnames(highlights)){
highlights[,"type"]}else{"h"},
col = if("color" %in% colnames(highlights)){
highlights[,"color"]}else{"#20BACE80"},
bty="n", lwd = 3, lend = 1)
}
#plotting the actual spectrum data points
points(spectrum[,1],spectrum[,2],type="h", bty="n", lwd = 1)
#reduce spectrum to only peaks within yrange to add labels:
spectrum <- spectrum[which(spectrum[,2] <= max(yrange)
& spectrum[,2] >= min(yrange)
),, drop = F]
if(nrow(spectrum) > k){
kn <- order(spectrum[,2], decreasing = T)[seq(k)]
spectrum <- spectrum[kn,, drop = F]
}
if(nrow(spectrum)>0){
if(!is.data.frame(spectrum)){
spectrum <- as.data.frame(spectrum, stringsAsFacotrs = F)
}
spectrum$label <- format(round(spectrum[,1],5),
nsmall = 5, scientific = F)
spectrum$color <- "blue"
}
#merge the automatically annotated peaks with labels
if(!is.null(labels)
&& nrow(labels)>0){
labels[,2] <- labels[,2]/norm
labels <- labels[which(labels[,1] <= max(xrange)
& labels[,1] >= min(xrange)
& labels[,2] <= max(yrange)
& labels[,2] >= min(yrange)
),, drop = F]
if(nrow(labels)>0){
if(is.null(labels$label)){
labels$label <- format(round(labels[,1],5),
nsmall = 5, scientific = F)
}
if(is.null(labels$color)){
labels$color <- "red"
}
if(nrow(spectrum) == 0){
spectrum <- labels
}else{
colnames(labels)[1:2] <- colnames(spectrum)[1:2]
spectrum <- rbind(labels[,c(colnames(labels)[1:2],
"label",
"color")],
spectrum[,c(colnames(labels)[1:2],
"label",
"color")])
spectrum <- spectrum[!duplicated(round(spectrum[,1],5)),]
}
}
}
if(nrow(spectrum) > 0 ){
par(xpd=NA)
# wordcloud::textplot(spectrum[,1], spectrum[,2],
# spectrum$label, cex=cx,new=FALSE,
# show.lines=TRUE,
# xlim = xrange,
# ylim = yrange)#, col=spectrum$color, rotate90 = T)
xcorr <- suppressWarnings({spread.labs(spectrum[,1],
1.13*strwidth("A", cex = cx),
maxiter=1000,
min=min(spectrum[,1]),
max=max(spectrum[,1]))})
segments(spectrum[,1],spectrum[,2]+0.01*max(yrange),
xcorr,spectrum[,2]+0.05*max(yrange), col="olivedrab4", lwd=0.8)
if(parseLabels){filabs <- parse(text = spectrum$label)}else{filabs <- spectrum$label}
text(xcorr,spectrum[,2]+0.055*max(yrange),
labels=filabs, col=spectrum$color,
srt=90,adj=c(0,0.3), cex=1*cx)
}
#show maximum intensity value at top left corner
text(min(xrange), max(yrange)+1.5*strheight("M"),
labels = format(maxi, scientific = T, digits =4), bty="n",
font = 2, cex=cx*1)
}
mjhelf/METABOseek documentation built on April 27, 2022, 5:13 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions parseTitle
Documented in parseTitle
#' parseTitle
#'
#' parse a scanInfo table into a title for a mass spectrum plot
#'
#' @return a character vector of length 1.
#'
#' @param scanInfo a data.frame as returned by \link{getScanInfo}()
#'
#' @export
parseTitle <- function(scanInfo){
if(is.null(scanInfo) ||nrow(scanInfo) == 0){
return("")
}
if(nrow(scanInfo) ==1){
return(
paste0(basename(scanInfo$filename), "#",
scanInfo$acquisitionNum,
" (", round(scanInfo$retentionTime/60,3), " min)",
if(scanInfo$precursorMZ != 0){
paste0("\nParent m/z: ",
format(round(scanInfo$precursorMZ,5),
nsmall = 5, scientific = F))}else{""},
collapse = " ")
)
}
if(all(scanInfo$msLevel == scanInfo$msLevel[1])){
return(
paste0(
if(length(unique(scanInfo$filename)) == 1){
paste0(scanInfo$filename[1],"#",
min(scanInfo$acquisitionNum),"-",
max(scanInfo$acquisitionNum),
"[",nrow(scanInfo)," scans]")
}else{
paste0("[",length(unique(scanInfo$filename)),
" files][",nrow(scanInfo)," scans]")
},
"(",
round(min(scanInfo$retentionTime)/60,3),
" - ",
round(max(scanInfo$retentionTime)/60,3),
" min)",
if(scanInfo$msLevel[1] > 1){
paste0("\nParent m/z: ",
round(mean(scanInfo$precursorMZ),5))}else{""}
)
)
}
return("Mixed different MS levels")
}
#' specplot2
#'
#' Plot an MS spectrum
#'
#' @param x mz coordinates
#' @param y intensity coordinates
#' @param spectrum matrix or data.frame, where the first column is m/z values,
#' and the second column are intensity values
#' @param norm normalize by
#' @param cx font size
#' @param k top k intensity peaks will be labeled
#' automatically with their mz values
#' @param fileName plot title
#' @param yrange y axis range
#' @param xrange x axis range
#' @param maxi max intensity to be plotted on side.
#' @param labels data.frame containing at least x and y coordinates,
#' plus optional columns: label and color
#' @param highlights matrix or data.frame, see \code{details}
#' @param mar margins passed to par()
#' @param ylab y axis label
#' @param ylabshift shift horizontal position of y axis label
#' @param parseLabels if TRUE, the \code{label} column in \code{labels} will
#' be parsed (using \code{\link[base]{parse}})
#'
#' @details
#' \describe{
#' \item{highlights}{matrix or data.frame with at the first two columns
#' containing x and y coordinates of peaks to highlight.
#' If \code{highlights} has an additional column called \code{color},
#' that column is expected to contain color values for the highlights.
#' If \code{highlights} has an additional column called \code{type},
#' that column is expected to contain point \code{type} values for the highlights,
#' as detailed in \link[graphics]{plot.default}.}
#' \item{labels}{
#' The first two columns of this data.frame will be assumed to be mz and intensity values, respectively.
#' If it only contains two columns, the first column values will be used as label text.
#' If a \code{label} column is present, that column will be used as peak labels.
#' If a \code{colors} column is present, that column will be used to define
#' the label color, otherwise it will be red.
#' }
#' \item{parseLabels}{
#' Parsing labels can be used to include subscript and
#' superscript elements in peak labels, but requires careful preparation
#' of the strings to be passed to \code{\link[base]{parse}}
#' }
#' }
#'
#' @return plots a spectrum view in the current plotting device
#'
#' @importFrom TeachingDemos spread.labs
#' @importFrom Hmisc minor.tick
#' @export
specplot2 <- function (x,
y,
spectrum,
norm= NULL,
cx=1,
k = 10,
fileName = "",
yrange = NULL,
xrange = NULL,
maxi = NULL,
labels = NULL,
highlights = NULL,
mar = c(3,4,6,1),
ylab = "Relative Intensity (%)",
ylabshift = 2,
parseLabels = F
){
if(!missing(spectrum) && !is.null(spectrum)){
if(is.null(xrange)){
xrange <- range(spectrum[,1])
sel <- TRUE
}else{
sel <- spectrum[,1] <= max(xrange) & spectrum[,1] >= min(xrange)
}
if(nrow(spectrum) == 0){
maxi <- 100
norm <- 1
}else{
#by default, scale largest y value in view to 100,
#to scale globally, set maxi to max(y) externally
if(is.null(maxi)){maxi <- if(!any(sel)
|| length(sel) == 0){100}else{max(spectrum[sel,2, drop = F])}}
if(!any(sel) || length(sel) == 0 || maxi == 0){
norm = 1
}
if(is.null(norm)){
norm = maxi/100
}
spectrum <- spectrum[sel,, drop = F]
}
spectrum[,2] <- spectrum[,2]/norm
}else{
if(is.null(xrange)){xrange = range(x)}
sel <- x <= max(xrange) & x >= min(xrange)
#by default, scale largest y value in view to 100,
#to scale globally, set maxi to max(y) externally
if(is.null(maxi)){maxi <- if(length(sel) == 0){1}else{max(y[sel])}}
if(length(sel) == 0 || maxi == 0){
norm = 1
}
if(is.null(norm)){
norm = maxi/100
}
spectrum <- data.frame(x=x[sel],
y=y[sel]/norm)
}
if(is.null(yrange)){yrange = c(0, maxi/norm)}
par(#oma=c(0,2,0,0), #oma causes issues with selectcallback
mar = mar,
xpd = FALSE, xaxs = "i", yaxs = "i")
PlotWindow(cx,
ylim = yrange,
xlim = xrange,
heading = fileName,
single = T,
par = F,
relto = norm,
ylab,
xlab = "m/z",
ysci = F,
textadj = 1,
ylabshift = ylabshift
)
if(!is.null(highlights)){
highlights[,2] <- highlights[,2]/norm
points(highlights[,1],highlights[,2],
type= if("type" %in% colnames(highlights)){
highlights[,"type"]}else{"h"},
col = if("color" %in% colnames(highlights)){
highlights[,"color"]}else{"#20BACE80"},
bty="n", lwd = 3, lend = 1)
}
#plotting the actual spectrum data points
points(spectrum[,1],spectrum[,2],type="h", bty="n", lwd = 1)
#reduce spectrum to only peaks within yrange to add labels:
spectrum <- spectrum[which(spectrum[,2] <= max(yrange)
& spectrum[,2] >= min(yrange)
),, drop = F]
if(nrow(spectrum) > k){
kn <- order(spectrum[,2], decreasing = T)[seq(k)]
spectrum <- spectrum[kn,, drop = F]
}
if(nrow(spectrum)>0){
if(!is.data.frame(spectrum)){
spectrum <- as.data.frame(spectrum, stringsAsFacotrs = F)
}
spectrum$label <- format(round(spectrum[,1],5),
nsmall = 5, scientific = F)
spectrum$color <- "blue"
}
#merge the automatically annotated peaks with labels
if(!is.null(labels)
&& nrow(labels)>0){
labels[,2] <- labels[,2]/norm
labels <- labels[which(labels[,1] <= max(xrange)
& labels[,1] >= min(xrange)
& labels[,2] <= max(yrange)
& labels[,2] >= min(yrange)
),, drop = F]
if(nrow(labels)>0){
if(is.null(labels$label)){
labels$label <- format(round(labels[,1],5),
nsmall = 5, scientific = F)
}
if(is.null(labels$color)){
labels$color <- "red"
}
if(nrow(spectrum) == 0){
spectrum <- labels
}else{
colnames(labels)[1:2] <- colnames(spectrum)[1:2]
spectrum <- rbind(labels[,c(colnames(labels)[1:2],
"label",
"color")],
spectrum[,c(colnames(labels)[1:2],
"label",
"color")])
spectrum <- spectrum[!duplicated(round(spectrum[,1],5)),]
}
}
}
if(nrow(spectrum) > 0 ){
par(xpd=NA)
# wordcloud::textplot(spectrum[,1], spectrum[,2],
# spectrum$label, cex=cx,new=FALSE,
# show.lines=TRUE,
# xlim = xrange,
# ylim = yrange)#, col=spectrum$color, rotate90 = T)
xcorr <- suppressWarnings({spread.labs(spectrum[,1],
1.13*strwidth("A", cex = cx),
maxiter=1000,
min=min(spectrum[,1]),
max=max(spectrum[,1]))})
segments(spectrum[,1],spectrum[,2]+0.01*max(yrange),
xcorr,spectrum[,2]+0.05*max(yrange), col="olivedrab4", lwd=0.8)
if(parseLabels){filabs <- parse(text = spectrum$label)}else{filabs <- spectrum$label}
text(xcorr,spectrum[,2]+0.055*max(yrange),
labels=filabs, col=spectrum$color,
srt=90,adj=c(0,0.3), cex=1*cx)
}
#show maximum intensity value at top left corner
text(min(xrange), max(yrange)+1.5*strheight("M"),
labels = format(maxi, scientific = T, digits =4), bty="n",
font = 2, cex=cx*1)
}
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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