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getEICs fix #31

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getEICs fix #31

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74dccee
Update fct_groupCorr.R to incorporate rt correction
trljcl May 16, 2018
fe97683
Update fct_groupCorr.R
trljcl May 21, 2018
9fa1136
fix getEICs() indexing fail on multiple samples
trljcl May 22, 2018
7ba8970
Update plotEIC.xsAnnotate.Rd
trljcl May 22, 2018
948c233
approximate rt vector for getAllPeakEICs
trljcl Mar 10, 2020
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50 changes: 28 additions & 22 deletions R/fct_groupCorr.R
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Original file line number Diff line number Diff line change
Expand Up @@ -93,9 +93,10 @@ setMethod("calcCiS", "xsAnnotate", function(object, EIC=EIC, corval=0.75,
#Set lower triangle to NA
res$r[lower.tri(res$r,diag = TRUE)] <- NA;
res$P[lower.tri(res$P,diag = TRUE)] <- NA;
res$n[lower.tri(res$n,diag = TRUE)] <- NA;

#Find peaks with have correlation higher corr_threshold and p <= 0.05
index <- which(( res$r > corval) & (res$P <= pval))
#Find peaks with have correlation higher corr_threshold and p <= 0.05 and > 3 comparisons
index <- which(( res$r > corval) & (res$P <= pval) & (res$n > 3))
if( (length(index) + cnt) >= nrow(resMat)){
#resize resMat
resMat <- rbind(resMat, create.matrix(max(length(index)+1,100000),4));
Expand Down Expand Up @@ -191,9 +192,10 @@ setMethod("calcCaS", "xsAnnotate", function(object, corval=0.75, pval=0.05,
#Set lower triangle to NA
res$r[lower.tri(res$r,diag = TRUE)] <- NA;
res$P[lower.tri(res$P,diag = TRUE)] <- NA;
res$n[lower.tri(res$n,diag = TRUE)] <- NA;

#Find peaks with have correlation higher corr_threshold and p <= 0.05
index <- which(( res$r > corval) & (res$P <= pval))
#Find peaks with have correlation higher corr_threshold and p <= 0.05 and > 3 comparisons
index <- which(( res$r > corval) & (res$P <= pval) & (res$n > 3))
if((length(index) + cnt) >= nrow(resMat)){
#resize resMat
size <- max(100000, (cnt+length(index) + 10000))
Expand Down Expand Up @@ -597,9 +599,10 @@ calcCL3 <- function(object, EIC=EIC, scantimes=scantimes, cor_eic_th=cor_eic_th,
#Set lower triangle to NA
res$r[lower.tri(res$r,diag = TRUE)] <- NA;
res$P[lower.tri(res$P,diag = TRUE)] <- NA;
res$n[lower.tri(res$n,diag = TRUE)] <- NA;

#Find peaks with have correlation higher corr_threshold and p <= 0.05
index <- which(( res$r > cor_eic_th) & (res$P <= 0.05))
#Find peaks with have correlation higher corr_threshold and p <= 0.05 and > 3 comparisons
index <- which(( res$r > cor_eic_th) & (res$P <= 0.05) & (res$n > 3))
if(length(index) > 0){
for( x in 1:(length(index))){
col <- index[x] %/% npi + 1;
Expand Down Expand Up @@ -750,6 +753,7 @@ getMaxScans <- function(object){
if(nfiles == 1){
if (file.exists(filepaths(object@xcmsSet)[1])) {
xraw <- xcmsRaw(filepaths(object@xcmsSet)[1],profstep=0)
xraw@scantime <- object@xcmsSet@rt$corrected[[1]]
maxscans <- length(xraw@scantime)
}else {
stop('Raw data file:',filepaths(object@xcmsSet)[1],' not found ! \n');
Expand All @@ -759,6 +763,7 @@ getMaxScans <- function(object){
for (f in 1:nfiles){
if(file.exists(filepaths(object@xcmsSet)[f])) {
xraw <- xcmsRaw(filepaths(object@xcmsSet)[f], profstep=0);
xraw@scantime <- object@xcmsSet@rt$corrected[[f]];
maxscans <- max(maxscans, length(xraw@scantime));
} else {
stop('Raw data file:',filepaths(object@xcmsSet)[f],' not found ! \n');
Expand Down Expand Up @@ -787,6 +792,7 @@ setMethod("getAllPeakEICs", "xsAnnotate", function(object, index=NULL){
if (file.exists(filepaths(object@xcmsSet)[1])) {

xraw <- xcmsRaw(filepaths(object@xcmsSet)[1],profstep=0)
xraw@scantime <- object@xcmsSet@rt$corrected[[1]]
maxscans <- length(xraw@scantime)
scantimes[[1]] <- xraw@scantime
pdata <- as.data.frame(object@xcmsSet@peaks)
Expand All @@ -805,15 +811,12 @@ setMethod("getAllPeakEICs", "xsAnnotate", function(object, index=NULL){

#na flag, stores if sample contains NA peaks
na.flag <- 0;
maxscans <- 0;

if (file.exists(filepaths(object@xcmsSet)[1])) {
xraw <- xcmsRaw(filepaths(object@xcmsSet)[1],profstep=0)
maxscans <- length(xraw@scantime)
} else {
stop('Raw data file:',filepaths(object@xcmsSet)[1],' not found ! \n');
}

# for approximation
maxscans <- max(sapply(object@xcmsSet@rt$corrected, length))
rtrange <- range(unlist(object@xcmsSet@rt$corrected), na.rm = TRUE)

rtvec <- seq(rtrange[1], rtrange[2], length.out = maxscans)

#generate EIC Matrix
EIC <- create.matrix(nrow(gval),maxscans)

Expand All @@ -832,13 +835,8 @@ setMethod("getAllPeakEICs", "xsAnnotate", function(object, index=NULL){
if (file.exists(filepaths(object@xcmsSet)[f])) {
#read sample
xraw <- xcmsRaw(filepaths(object@xcmsSet)[f], profstep=0);
maxscans.tmp <- length(xraw@scantime);
xraw@scantime <- object@xcmsSet@rt$corrected[[f]];
scantimes[[f]] <- xraw@scantime
if(maxscans.tmp > maxscans){
#increase columns of EIC matrix
EIC <- cbind(EIC,create.matrix(nrow(gval),maxscans.tmp - maxscans));
maxscans <- maxscans.tmp;
}

pdata <- as.data.frame(object@xcmsSet@peaks[gval[idx.peaks,f],,drop=FALSE]) # data for peaks from file f

Expand All @@ -848,7 +846,12 @@ setMethod("getAllPeakEICs", "xsAnnotate", function(object, index=NULL){
}

#Generate raw data according to peak data
EIC[idx.peaks,] <- getEIC4Peaks(xraw,pdata,maxscans)
EIC.tmp <- CAMERA:::getEIC4Peaks(xraw, pdata)
EIC.tmp[is.na(EIC.tmp)] <- 0
EIC.tmp <- t(apply(EIC.tmp, 1, function(a) {approx(x = xraw@scantime, y = a, xout = rtvec, rule = 2)$y}))
EIC.tmp[EIC.tmp == 0] <- NA
EIC[idx.peaks, ] <- EIC.tmp
rm(EIC.tmp)

} else {
stop('Raw data file:',filepaths(object@xcmsSet)[f],' not found ! \n')
Expand Down Expand Up @@ -972,6 +975,7 @@ getAllEICs <- function(xs,index=NULL,file=NULL) {
for (f in 1:nfiles){
# cat('Reading raw data file:',filepaths(xs)[f])
xraw <- xcmsRaw(filepaths(xs)[f],profstep=0)
xraw@scantime <- xs@rt$corrected[[f]]
# cat(',', length(xraw@scantime),'scans. \n')
maxscans <- max(maxscans,length(xraw@scantime))
scantimes[[f]] <- xraw@scantime
Expand All @@ -981,6 +985,7 @@ getAllEICs <- function(xs,index=NULL,file=NULL) {
if (file.exists(filepaths(xs)[f])) {
# cat('Reading raw data file:',filepaths(xs)[f],'\n')
xraw <- xcmsRaw(filepaths(xs)[f],profstep=0)
xraw@scantime <- xs@rt$corrected[[f]]
# cat('Generating EIC\'s .. \n')
idx.peaks <- which(index == f);
if(length(idx.peaks)>0){
Expand All @@ -998,6 +1003,7 @@ getAllEICs <- function(xs,index=NULL,file=NULL) {
if (file.exists(filepaths(xs)[1])) {
#cat('Reading raw data file:',filepaths(xs)[1],'\n')
xraw <- xcmsRaw(filepaths(xs)[1],profstep=0)
xraw@scantime <- xs@rt$corrected[[1]]
#cat('Generating EIC\'s .. \n')
maxscans <- length(xraw@scantime)
scantimes[[1]] <- xraw@scantime
Expand Down
20 changes: 10 additions & 10 deletions R/xsVisualise.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,21 +10,24 @@ setMethod("plotEICs", "xsAnnotate", function(object,
smpls <- unique(object@psSamples[pspec])

xeic <- new("xcmsEIC");
xeic@eic <- vector("list", length(pspec))
xeic@rtrange <- matrix(nrow=length(pspec), ncol=2)
xeic@mzrange <- matrix(nrow=length(pspec), ncol=2)
#iterator for ps-grp
pcpos <- 1;
cnt <- 0;
#one second overlap
rtmargin <- 1;

for (a in seq(along=smpls)) { ## sample-wise EIC collection
#read rawData into one xcmsRaw
xraw <- xcmsRaw(object@xcmsSet@filepaths[smpls[a]], profmethod=method)
xraw@scantime <- object@xcmsSet@rt$corrected[[smpls[a]]]

pspecS <- pspec[which(object@psSamples[pspec] == smpls[a])]
## getting ALL peaks from the current sample (not that bad)
peaks <- CAMERA:::getPeaks(object@xcmsSet, smpls[a])
eic <- lapply (pspecS, function(pc) {
invisible(lapply (pspecS, function(pc) {
cnt <<- cnt + 1
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<<- immediately jumps at me. Any chance to avoid that ?

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Not sure why this would be an issue, becuase as I understand it <<- applies to the parent environment, which in this case is PlotEICs() where cnt is assigned at line 17 (and so not to the the global environment)?

pidx <- object@pspectra[[pc]]
pks <- peaks[pidx, , drop=FALSE]
gks <- object@groupInfo[pidx, , drop=FALSE]
Expand All @@ -38,14 +41,11 @@ setMethod("plotEICs", "xsAnnotate", function(object,
eic <- xcms:::getEIC(xraw, rtrange=pks[, c("rtmin", "rtmax"), drop=FALSE],
mzrange=pks[, c("mzmin", "mzmax"), drop=FALSE])
#write resulting bounding box into xcmsEIC
xeic@rtrange[pcpos, ] <<- bbox[c("rtmin","rtmax")]
xeic@mzrange[pcpos, ] <<- bbox[c("mzmin","mzmax")]
cat("-->", pcpos, "\n")
pcpos <<- pcpos+1

eic@eic[[1]]
})
xeic@eic <- c(xeic@eic, eic)
xeic@rtrange[pc, ] <<- bbox[c("rtmin","rtmax")]
xeic@mzrange[pc, ] <<- bbox[c("mzmin","mzmax")]
cat("--> ", pc, " (", cnt, " of ", length(pspec), ")", "\n", sep = "")
xeic@eic[[pc]] <<- eic@eic[[1]]
}))
}
names(xeic@eic) <- paste("Pseudospectrum ", pspec, sep="")

Expand Down
2 changes: 0 additions & 2 deletions man/plotEIC.xsAnnotate.Rd
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,6 @@
\item{object = "xsAnnotate"}{
\code{
plotEICs(object,
xraw,
pspec=1:length(object@pspectra),
maxlabel=0, sleep=0)}
}
Expand All @@ -24,7 +23,6 @@
}
\arguments{
\item{object}{the \code{xsAnnotate} object}
\item{xraw}{\code{xcmsRaw} object underlying the the xsAnnotate}
\item{maxlabel}{How many m/z labels to print}
\item{sleep}{seconds to pause between plotting EICs}
\item{...}{other graphical parameters}
Expand Down