├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── compensate.R ├── extract.R ├── postprocessUtilites.R ├── read.R └── write.R ├── README.mediawiki ├── cytofCore.Rproj ├── inst └── automator │ ├── R │ ├── ExtractIMD.R │ └── Subtract100.R │ └── apps │ ├── Concatenate.app │ └── Contents │ │ ├── Info.plist │ │ ├── MacOS │ │ └── Application Stub │ │ ├── Resources │ │ ├── AutomatorApplet.icns │ │ ├── Dutch.lproj │ │ │ └── ApplicationStub.nib │ │ ├── English.lproj │ │ │ └── ApplicationStub.nib │ │ ├── French.lproj │ │ │ └── ApplicationStub.nib │ │ ├── German.lproj │ │ │ └── ApplicationStub.nib │ │ ├── Italian.lproj │ │ │ └── ApplicationStub.nib │ │ ├── Japanese.lproj │ │ │ └── ApplicationStub.nib │ │ ├── Spanish.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ar.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ca.lproj │ │ │ └── ApplicationStub.nib │ │ ├── cs.lproj │ │ │ └── ApplicationStub.nib │ │ ├── da.lproj │ │ │ └── ApplicationStub.nib │ │ ├── el.lproj │ │ │ └── ApplicationStub.nib │ │ ├── fi.lproj │ │ │ └── ApplicationStub.nib │ │ ├── he.lproj │ │ │ └── ApplicationStub.nib │ │ ├── hr.lproj │ │ │ └── ApplicationStub.nib │ │ ├── hu.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ko.lproj │ │ │ └── ApplicationStub.nib │ │ ├── no.lproj │ │ │ └── ApplicationStub.nib │ │ ├── pl.lproj │ │ │ └── ApplicationStub.nib │ │ ├── pt.lproj │ │ │ └── ApplicationStub.nib │ │ ├── pt_PT.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ro.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ru.lproj │ │ │ └── ApplicationStub.nib │ │ ├── sk.lproj │ │ │ └── ApplicationStub.nib │ │ ├── sv.lproj │ │ │ └── ApplicationStub.nib │ │ ├── th.lproj │ │ │ └── ApplicationStub.nib │ │ ├── tr.lproj │ │ │ └── ApplicationStub.nib │ │ ├── uk.lproj │ │ │ └── ApplicationStub.nib │ │ ├── zh_CN.lproj │ │ │ └── ApplicationStub.nib │ │ └── zh_TW.lproj │ │ │ └── ApplicationStub.nib │ │ └── document.wflow │ ├── Extract IMD.app │ └── Contents │ │ ├── Info.plist │ │ ├── MacOS │ │ └── Application Stub │ │ ├── Resources │ │ ├── AutomatorApplet.icns │ │ ├── Dutch.lproj │ │ │ └── ApplicationStub.nib │ │ ├── English.lproj │ │ │ └── ApplicationStub.nib │ │ ├── French.lproj │ │ │ └── ApplicationStub.nib │ │ ├── German.lproj │ │ │ └── ApplicationStub.nib │ │ ├── Italian.lproj │ │ │ └── ApplicationStub.nib │ │ ├── Japanese.lproj │ │ │ └── ApplicationStub.nib │ │ ├── Spanish.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ar.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ca.lproj │ │ │ └── ApplicationStub.nib │ │ ├── cs.lproj │ │ │ └── ApplicationStub.nib │ │ ├── da.lproj │ │ │ └── ApplicationStub.nib │ │ ├── el.lproj │ │ │ └── ApplicationStub.nib │ │ ├── fi.lproj │ │ │ └── ApplicationStub.nib │ │ ├── he.lproj │ │ │ └── ApplicationStub.nib │ │ ├── hr.lproj │ │ │ └── ApplicationStub.nib │ │ ├── hu.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ko.lproj │ │ │ └── ApplicationStub.nib │ │ ├── no.lproj │ │ │ └── ApplicationStub.nib │ │ ├── pl.lproj │ │ │ └── ApplicationStub.nib │ │ ├── pt.lproj │ │ │ └── ApplicationStub.nib │ │ ├── pt_PT.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ro.lproj │ │ │ └── ApplicationStub.nib │ │ ├── ru.lproj │ │ │ └── ApplicationStub.nib │ │ ├── sk.lproj │ │ │ └── ApplicationStub.nib │ │ ├── sv.lproj │ │ │ └── ApplicationStub.nib │ │ ├── th.lproj │ │ │ └── ApplicationStub.nib │ │ ├── tr.lproj │ │ │ └── ApplicationStub.nib │ │ ├── uk.lproj │ │ │ └── ApplicationStub.nib │ │ ├── zh_CN.lproj │ │ │ └── ApplicationStub.nib │ │ └── zh_TW.lproj │ │ │ └── ApplicationStub.nib │ │ └── document.wflow │ └── Subtract100.app │ └── Contents │ ├── Info.plist │ ├── MacOS │ └── Application Stub │ ├── Resources │ ├── AutomatorApplet.icns │ ├── Dutch.lproj │ │ └── ApplicationStub.nib │ ├── English.lproj │ │ └── ApplicationStub.nib │ ├── French.lproj │ │ └── ApplicationStub.nib │ ├── German.lproj │ │ └── ApplicationStub.nib │ ├── Italian.lproj │ │ └── ApplicationStub.nib │ ├── Japanese.lproj │ │ └── ApplicationStub.nib │ ├── Spanish.lproj │ │ └── ApplicationStub.nib │ ├── ar.lproj │ │ └── ApplicationStub.nib │ ├── ca.lproj │ │ └── ApplicationStub.nib │ ├── cs.lproj │ │ └── ApplicationStub.nib │ ├── da.lproj │ │ └── ApplicationStub.nib │ ├── el.lproj │ │ └── ApplicationStub.nib │ ├── fi.lproj │ │ └── ApplicationStub.nib │ ├── he.lproj │ │ └── ApplicationStub.nib │ ├── hr.lproj │ │ └── ApplicationStub.nib │ ├── hu.lproj │ │ └── ApplicationStub.nib │ ├── ko.lproj │ │ └── ApplicationStub.nib │ ├── no.lproj │ │ └── ApplicationStub.nib │ ├── pl.lproj │ │ └── ApplicationStub.nib │ ├── pt.lproj │ │ └── ApplicationStub.nib │ ├── pt_PT.lproj │ │ └── ApplicationStub.nib │ ├── ro.lproj │ │ └── ApplicationStub.nib │ ├── ru.lproj │ │ └── ApplicationStub.nib │ ├── sk.lproj │ │ └── ApplicationStub.nib │ ├── sv.lproj │ │ └── ApplicationStub.nib │ ├── th.lproj │ │ └── ApplicationStub.nib │ ├── tr.lproj │ │ └── ApplicationStub.nib │ ├── uk.lproj │ │ └── ApplicationStub.nib │ ├── zh_CN.lproj │ │ └── ApplicationStub.nib │ └── zh_TW.lproj │ │ └── ApplicationStub.nib │ └── document.wflow └── man ├── cytofCore.extract.R.Rd ├── cytofCore.read.conf.Rd ├── cytofCore.read.imd.Rd └── cytofCore.write.FCS.Rd /.gitignore: -------------------------------------------------------------------------------- 1 | *.swp 2 | *.so 3 | *.o 4 | config.log 5 | config.status 6 | a.out.dSYM 7 | .DS_Store 8 | .Rproj.user 9 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: cytofCore 2 | Title: cytofCore: Analysis tools for CyToF Mass Cytometer Data 3 | Version: 0.4 4 | Author: R. Bruggner, M. Linderman, R. Finck 5 | Description: Provides tools for working with CyToF Mass Cytometer Data 6 | Maintainer: R. Bruggner 7 | Depends: R (>= 2.8.1), flowCore 8 | Suggests: tcltk, XML 9 | Imports: flowCore 10 | License: GPL-2 11 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | export( 2 | "cytofCore.read.imd", 3 | "cytofCore.read.imd.xml", 4 | "cytofCore.read.conf", 5 | "cytofCore.write.FCS", 6 | "cytofCore.extract.R", 7 | "cytofCore.combineChannels", 8 | "cytofCore.subtract", 9 | "cytofCore.concatenateDirectoryFiles", 10 | "cytofCore.updateFlowFrameKeywords", 11 | "cytofCore.applyFileCompensation", 12 | "cytofCore.batchFileCompensate", 13 | "cytofCore.updatePanel", 14 | "cytofCore.rewriteImdCoeffs", 15 | "cytofCore.copyImdXml", 16 | "cytofCore.read.tof.calibration", 17 | cytofCore.read.rd8.cytof2, 18 | cytofCore.read.rd8.cytof1 19 | ) 20 | -------------------------------------------------------------------------------- /R/compensate.R: -------------------------------------------------------------------------------- 1 | applyCompensation = function(flowFrame,compMatrix){ 2 | return(compensate(flowFrame,compMatrix)) 3 | } 4 | 5 | cytofCore.applyFileCompensation = function(inputFCSFile,inputCompFile,outputFile,row.names=1,skip=0){ 6 | flowFrame = read.FCS(inputFCSFile) 7 | compMatrix = read.csv(inputCompFile,check.names=F,header=T,row.names=row.names,skip=skip) 8 | compedFrame = applyCompensation(flowFrame,compMatrix) 9 | write.FCS(compedFrame,filename=outputFile) 10 | } 11 | 12 | cytofCore.batchFileCompensate = function(inputFCSDirectory,inputCompDirectory,outputDirectory,fcsFiles,compFiles){ 13 | if ((length(compFiles)=!1)||(length(compFiles)!=length(fcsFiles))){ 14 | stop("Must provide a single comp file or a comp file for each fcs file.") 15 | } 16 | if (length(compFiles)==1){ 17 | compFiles = rep(compFile,length(fcsFiles)) 18 | } 19 | for (i in 1:length(fcsFiles)){ 20 | fcsFile = fcsFiles[i] 21 | compFile = compFiles[i] 22 | print("Comping",fcsFile,"with",compFile) 23 | cytofCore.applyFileCompensation(inputFCSFile=file.path(inputFCSDirectory,fcsFile), 24 | inputCompFile=file.path(inputCompDirectory,compFile), 25 | outputFile=file.path(outputDirectory,fcsFile)) 26 | } 27 | } 28 | 29 | -------------------------------------------------------------------------------- /R/extract.R: -------------------------------------------------------------------------------- 1 | cytofCore.extract.cells <- function(data, cols=NULL, thresh=10.0, sigma=3, num_sigma=3, noise.min.length=30, freq=77000) { 2 | if (!is.matrix(data)) { 3 | stop("'data' must be a matrix"); 4 | } 5 | 6 | if (is.null(cols)) { 7 | cols <- 1:ncol(data) 8 | } else { 9 | cols <- match(cols,colnames(data)) 10 | if (any(is.na(cols))) { 11 | stop("Invalid column specifier") 12 | } 13 | } 14 | 15 | # Apply gaussian filter to total intensity 16 | coeff <- dnorm((-num_sigma*sigma):(num_sigma*sigma),sd=sigma) 17 | d <- stats::filter(ts(rowSums(data[,cols]),frequency=freq), coeff, method="convolution", sides=2) 18 | 19 | # Cells are runs of data >= threshold, while noise is preceding region 20 | runs <- rle(as.vector(d >= thresh)) 21 | cells <- which(runs$value) 22 | 23 | found <- matrix(nrow=length(cells),ncol=length(cols)+3) 24 | found[,1] <- (cumsum(runs$lengths))[cells-1] + 1 # Leading push (+1 b/c R is "1" indexed) 25 | found[,2] <- found[,1]/freq*1000 26 | found[,3] <- runs$lengths[cells] # Cell length 27 | for (i in 1:nrow(found)) { 28 | cell_range <- seq(found[i,1],length.out=found[i,3]) 29 | found[i,4:ncol(found)] <- colSums(data[cell_range,cols]) # Integrate raw data for cell 30 | } 31 | colnames(found) <- c("Leading_Push", "Time", "Cell_length",colnames(data)[cols]) 32 | 33 | noise <- matrix(nrow=length(cells),ncol=length(cols)+2) 34 | noise[,1] <- (cumsum(runs$lengths))[cells-2] + 1 # Leading push for region preceding cell 35 | noise[,2] <- runs$lengths[cells-1] # Noise region duration 36 | for (i in 1:nrow(noise)) { 37 | if (noise[i,2] > 1) { 38 | noise_range <- seq(noise[i,1],length.out=noise[i,2]) 39 | noise[i,3:ncol(noise)] <- colSums(data[noise_range,cols]) / noise[i,2] # Produce per push noise estimate 40 | } else { 41 | noise[i,3:ncol(noise)] <- data[noise[i,1],cols] 42 | } 43 | } 44 | noise <- subset(noise, noise[,2] > noise.min.length) 45 | colnames(noise) <- c("Leading_Push", "Duration",colnames(data)[cols]) 46 | 47 | list(cells=found, noise=noise, intensity=d) 48 | } 49 | 50 | cytofCore.filter.cells <- function(cells) { 51 | # Filter out cells with multiple peaks 52 | fail <- c() 53 | for (i in 1:nrow(cells$cells)) { 54 | beg <- cells$cells[i,1] 55 | len <- cells$cells[i,3] 56 | 57 | slope <- cells$intensity[seq(beg+1,length.out=len)] - cells$intensity[seq(beg,length.out=len)] 58 | runs <- rle(slope > 0) 59 | if (length(runs$values) > 2) { # More than one zero crossing ... 60 | fail <- c(fail, i) 61 | } 62 | } 63 | return(fail) 64 | } 65 | 66 | cytofCore.extract.R <- function(imd, conf, 67 | pulse_thresh=3.0, num_pushes=NULL, thresh=10.0, sigma=3, num_sigma=3, min_length=10, max_length=75, noise.subtraction=TRUE, 68 | noise.min.length=30, slope.filter=TRUE, freq=77000) { 69 | 70 | dual <- cytofCore.read.imd(imd, conf=conf, pulse_thresh=pulse_thresh, num_pushes=num_pushes) 71 | cell <- cytofCore.extract.cells(dual$dual, thresh=thresh, sigma=sigma, num_sigma=num_sigma, noise.min.length=noise.min.length, freq=freq) 72 | 73 | cell$cells <- subset(cell$cells, cell$cells[,"Cell_length"] >= min_length & cell$cells[,"Cell_length"] < max_length) 74 | 75 | quality <- rep(1., nrow(cell$cells)) 76 | if (slope.filter) { 77 | quality[cytofCore.filter.cells(cell)] <- 0.0 78 | } 79 | 80 | if (noise.subtraction) { 81 | cell$noise <- rbind(matrix(0., nrow=1, ncol=ncol(cell$noise)),cell$noise) 82 | noise.idxs <- findInterval(cell$cells[,"Leading_Push"],cell$noise[,"Leading_Push"]) 83 | # 3 is start of analyte columns for noise, 4 is start for cells 84 | cell$cells[,4:ncol(cell$cells)] <- 85 | cell$cells[,4:ncol(cell$cells)] - cell$cells[,"Cell_length"]*cell$noise[noise.idxs,3:ncol(cell$noise)] 86 | } 87 | 88 | list(cells.found=cell$cells,quality=quality) 89 | } 90 | 91 | 92 | 93 | -------------------------------------------------------------------------------- /R/postprocessUtilites.R: -------------------------------------------------------------------------------- 1 | cytofCore.updateFlowFrameKeywords = function(flowFrame){ 2 | 3 | params = parameters(flowFrame) 4 | pdata = pData(params) 5 | for (i in 1:ncol(flowFrame)){ 6 | s = paste("$P",i,"S",sep=""); 7 | n = paste("$P",i,"N",sep=""); 8 | r = paste("$P",i,"R",sep=""); 9 | b = paste("$P",i,"B",sep=""); 10 | e = paste("$P",i,"E",sep=""); 11 | keyval=list(); 12 | keyval[[s]] = colnames(flowFrame)[i]; 13 | keyval[[n]] = colnames(flowFrame)[i]; 14 | keyval[[r]] = ceiling(max(exprs(flowFrame)[,i])-min(exprs(flowFrame)[,i])) 15 | keyval[[b]] = 32; 16 | keyval[[e]] = "0,0"; 17 | keyword(flowFrame) = keyval; 18 | 19 | 20 | pdata[i,"minRange"]=min(exprs(flowFrame)[,i]) 21 | pdata[i,"maxRange"]=max(exprs(flowFrame)[,i]) 22 | 23 | } 24 | pData(params)=pdata 25 | parameters(flowFrame)=params 26 | 27 | # keyval[["$DATATYPE"]] <- "F" 28 | return(flowFrame) 29 | } 30 | 31 | cytofCore.combineChannels = function(flowFrame,channelList,newName=NULL){ 32 | if (!all(channelList %in% colnames(flowFrame))){ 33 | offending = which(!(channelList %in% colnames(flowFrame))) 34 | stop( paste("Channel(s)",paste(channelList[offending],collapse=","),"not found in frame.") ) 35 | } 36 | 37 | # Add data in combined channels 38 | combinedValues = apply(exprs(flowFrame)[,channelList],1,sum) 39 | 40 | channelNumber = ncol(flowFrame)+1 41 | channelId = paste("$P",channelNumber,sep=""); 42 | if (is.null(newName)){ 43 | newName = paste("channel",paste(channelList,collapse="-"),"combined",sep="_"); 44 | } 45 | 46 | 47 | params = parameters(flowFrame) 48 | pdata = pData(params) 49 | plist = matrix(c(newName,newName,ceiling(max(combinedValues)-min(combinedValues)),floor(min(combinedValues)),ceiling(max(combinedValues)))); 50 | rownames(plist) = c("name","desc","range","minRange","maxRange"); 51 | colnames(plist) = c(channelId); 52 | pdata = rbind(pdata,t(plist)) 53 | pData(params) = pdata 54 | 55 | return(cytofCore.updateFlowFrameKeywords(flowFrame(exprs=cbind(exprs(flowFrame), `colnames<-`(cbind(combinedValues), newName)),parameters=params,description=description(flowFrame)))) 56 | } 57 | 58 | cytofCore.subtract = function(flowFrame,value=100,exclude=c(1,2)){ 59 | 60 | if (length(exclude)>0){ 61 | if (!is.numeric(exclude)){ 62 | if (!all(exclude %in% colnames(flowFrame))){ 63 | offending = which(!(exclude %in% colnames(flowFrame))) 64 | stop( paste("Channel(s)",paste(exclude[offending],collapse=","),"not found in frame.") ) 65 | } 66 | } else { 67 | exclude = colnames(flowFrame)[exclude]; 68 | } 69 | } 70 | 71 | subtractCols = setdiff(colnames(flowFrame),exclude) 72 | exprs(flowFrame)[,subtractCols] = exprs(flowFrame)[,subtractCols]-value 73 | 74 | return(cytofCore.updateFlowFrameKeywords(flowFrame)) 75 | } 76 | 77 | cytofCore.concatenateDirectoryFiles = function(inputDir,outputDir=NULL,pattern=NULL,overwrite=F,timeParam="time"){ 78 | currentwd = getwd(); 79 | 80 | if (is.null(outputDir)){ 81 | outputDir = inputDir; 82 | } 83 | if (!file.exists(inputDir)){ 84 | stop(paste("Input Directory",inputDir,"not found.")) 85 | } 86 | if (!file.exists(outputDir)){ 87 | stop(paste("Output Directory",outputDir,"not found.")) 88 | } 89 | 90 | setwd(inputDir); 91 | if (is.null(pattern)){ 92 | outputFileName="combined.fcs"; 93 | } else { 94 | outputFileName = paste(paste(pattern,collapse="-"),"_combined.fcs",sep="") 95 | } 96 | 97 | if (file.exists(outputFileName) && !overwrite){ 98 | stop(paste("File ",outputFileName," already exists in dir ",outputDir,". Set overwrite argument to TRUE or remove file first.",sep="")) 99 | } 100 | 101 | fcsFiles = list.files(inputDir, pattern=".fcs$", ignore.case=TRUE) 102 | 103 | matched = c(1:length(fcsFiles)); 104 | for (match in pattern){ 105 | matched=intersect(matched,grep(match,fcsFiles)) 106 | } 107 | combineFiles = fcsFiles[matched] 108 | 109 | begin=T 110 | for (file in combineFiles){ 111 | cat(paste("Adding",file,"\n")); 112 | if (begin){ 113 | fcs = read.FCS(file) 114 | combinedData = exprs(fcs); 115 | columns = colnames(combinedData) 116 | timeCol = which(tolower(columns) == "time") 117 | if (!length(timeCol)){ 118 | stop(paste("Time Column",timeParam,"not found for file",file)); 119 | } 120 | fcsDescription = description(fcs) 121 | channels = parameters(fcs)$desc 122 | begin=F 123 | 124 | } else { 125 | tmpData = exprs(read.FCS(file)); 126 | # check that column names are the same before concatenating 127 | if (any(colnames(tmpData) != columns)) { 128 | stop(paste("File", file, "does not have matching panel.")); 129 | } 130 | tmpData[,timeCol] = tmpData[,timeCol]+(max(combinedData[,timeCol])+round((max(combinedData[,timeCol])-min(combinedData[,timeCol]))/nrow(combinedData))) 131 | combinedData = rbind(combinedData,tmpData) 132 | } 133 | } 134 | 135 | # copy the channel descriptions from the first file 136 | cytofCore.write.FCS(combinedData, outputFileName, what="numeric", channelDescription=channels, 137 | referenceDescription=fcsDescription, oldDescription=fcsDescription) 138 | gc() 139 | setwd(currentwd); 140 | return(paste(outputDir,"->",outputFileName)) 141 | } 142 | 143 | cytofCore.concatenateFiles = function(fcsFiles,timeCol="Time"){ 144 | begin=T 145 | for (file in fcsFiles){ 146 | if (!file.exists(file)){ 147 | stop(paste(file,"Not Found! Stopping.")) 148 | } 149 | cat(paste("Adding",file,"\n")); 150 | if (begin){ 151 | combinedData = exprs(read.FCS(file)); 152 | if (!(timeCol %in% colnames(combinedData))){ 153 | stop(paste("Time Column",timeCol,"not found for file",file)); 154 | } 155 | begin=F 156 | } else { 157 | tmpData = exprs(read.FCS(file)); 158 | if (!all(colnames(tmpData)==colnames(combinedData))){ 159 | stop(paste("File names in files do not match.",colnames(tmpData),colnames(combinedData),sep="\n")) 160 | } 161 | if (!(timeCol %in% colnames(tmpData))){ 162 | stop(paste("Time Column",timeCol,"not found for file",file)); 163 | } 164 | tmpData[,timeCol] = tmpData[,timeCol]+(max(combinedData[,timeCol])+round((max(combinedData[,timeCol])-min(combinedData[,timeCol]))/nrow(combinedData))) 165 | combinedData = rbind(combinedData,tmpData) 166 | } 167 | } 168 | outputFileName = paste(dirname(fcsFiles[1]),"/concatenated_",gsub("\\s+","_",date()),".fcs",sep="") 169 | write.FCS(cytofCore.updateFlowFrameKeywords(flowFrame(exprs=combinedData)),outputFileName); 170 | return(outputFileName) 171 | } 172 | 173 | cytofCore.updatePanel = function(templateFile=NULL, fcsFolder=NULL){ 174 | if (is.null(templateFile) || is.null(fcsFolder)) { 175 | library("tcltk") 176 | } 177 | 178 | if (is.null(templateFile)) { 179 | #select template file, which has list of metals you want to include and their desired marker names 180 | Filters <- matrix(c("template", ".txt","template", ".TXT", "template",".fcs","template",".FCS","template",".csv","template","CSV"), 6, 2, byrow = TRUE) 181 | templateFile<- tk_choose.files(caption="Select template file", multi=FALSE, filters=Filters) 182 | } 183 | 184 | if (!file.exists(templateFile)) { 185 | stop(paste("Template file", templateFile, "not found.")) 186 | } 187 | 188 | templateExt = substr(templateFile,nchar(templateFile)-2,nchar(templateFile)) 189 | 190 | #read in metal and marker list from template file 191 | if (templateExt=="csv" || templateExt=="CSV") { 192 | data =read.csv(templateFile, header=FALSE) 193 | channels=as.character(data[,1]) 194 | markers=as.character(data[,2]) 195 | } else if (templateExt=="txt" || templateExt=="TXT") { 196 | data=read.table(templateFile, header=FALSE) 197 | channels=as.character(data[,1]) 198 | markers=as.character(data[,2]) 199 | } else if (templateExt=="fcs" || templateExt=="FCS") { 200 | data=read.FCS(templateFile) 201 | channels=as.character(parameters(data)$name) 202 | markers=as.character(parameters(data)$desc) 203 | } 204 | 205 | 206 | #for simplicity, copy over the channel values when the markers are empty 207 | for (i in 1:length(markers)) { 208 | if ((nchar(markers[i]) == 0) || is.na(markers[i])) { 209 | markers[i]=channels[i] 210 | } 211 | } 212 | 213 | #select folder of FCS files to relabel 214 | if (is.null(fcsFolder)) { 215 | fcsFolder<-tk_choose.dir() 216 | } 217 | 218 | newFolder<-file.path(fcsFolder,"relabeled") 219 | dir.create(newFolder) 220 | fcsFiles<-list.files(path=fcsFolder, pattern=".fcs$", ignore.case = TRUE) 221 | 222 | addZeroCol<-matrix(0,ncol=length(channels)) #keep track of whether to add missing column for all files 223 | for (file in fcsFiles) { 224 | oldFile=read.FCS(file.path(fcsFolder,file)) 225 | oldChannels=as.character(parameters(oldFile)$name) 226 | oldData=exprs(oldFile) 227 | newData=matrix(data=0,nrow=nrow(oldData),ncol=length(channels)) 228 | 229 | keepCols=matrix(TRUE,ncol=length(channels)) #keep track of columns to include in final matrix 230 | for (i in 1:length(channels)) { 231 | ind=grep(paste("\\Q",channels[i],"\\E",sep=""),oldChannels) 232 | if (length(ind)==1) { #found this template metal in this fcs file 233 | newData[,i]=oldData[,ind] 234 | } else if (addZeroCol[i]==0) { #haven't decided yet whether to create dummy column 235 | print(paste("Channel", channels[i], "was not found in",file,"!")) 236 | yn=readline("Do you want to create a column of zeros in its place? y/n: ") 237 | 238 | allone=readline("Do you want to apply this to all FCS files in this folder? y/n: ") 239 | 240 | if (yn=="y" && allone=="y") { #create dummy column in this and all files 241 | addZeroCol[i]=1 242 | } else if (yn=="n" && allone=="y") { #don't create dummy column in any file 243 | addZeroCol[i]=-1 244 | keepCols[i]=FALSE 245 | } else if (yn=="n") {#don't create dummy column but only in this file 246 | keepCols[i]=FALSE 247 | } 248 | } else if (addZeroCol[i]==-1) { #previously decided not to create this dummy column 249 | keepCols[i]=FALSE 250 | } 251 | 252 | } 253 | 254 | newData=newData[,keepCols] 255 | newChannels=channels[keepCols] 256 | newMarkers=markers[keepCols] 257 | 258 | colnames(newData) = newChannels 259 | 260 | print(paste("Writing",file)) 261 | 262 | referenceDescription = NULL 263 | if (templateExt=="fcs" || templateExt=="FCS") { 264 | referenceDescription=description(data) 265 | } 266 | 267 | cytofCore.write.FCS(newData,file.path(newFolder,file),channelDescriptions=newMarkers,referenceDescription=referenceDescription,oldDescription=description(oldFile)) 268 | } 269 | 270 | } 271 | 272 | cytofCore.averageDdCoefficients = function(folder,masses) { 273 | #average slopes and intercepts across a set of conf files for selected masses 274 | fileList=list.files(path=folder, pattern=".conf$") 275 | slopes=matrix(ncol=length(masses),nrow=length(fileList)) 276 | intercepts=matrix(ncol=length(masses),nrow=length(fileList)) 277 | for (i in 1:length(fileList)) { 278 | conf=cytofCore.read.conf(file.path(folder,fileList[i])) 279 | if (i==1) { 280 | massesMeasured=conf$Mass 281 | } else if (any(conf$Mass != massesMeasured)) { 282 | stop("Panels of conf files are not consistent.") 283 | } 284 | slopes[i,]=approx(conf$Mass,conf$Slope,masses,method="linear",rule=2)$y 285 | intercepts[i,]=approx(conf$Mass,conf$Intercept,masses,method="linear",rule=2)$y 286 | } 287 | results=rbind(colMeans(slopes),colMeans(intercepts)) 288 | colnames(results)=masses 289 | rownames(results)=c("slopes","intercepts") 290 | return(results) 291 | } 292 | 293 | cytofCore.rewriteImdCoeffs = function(imdFile,confFolder) { 294 | #rewrite the slopes and intercepts in the dual calibration as the average from a set of conf files 295 | 296 | library("XML") 297 | 298 | # extract xml from tail of imd 299 | imd <- file(imdFile, "r+b") 300 | if (!isSeekable(imd)) { 301 | stop("Cannot seek in specified file or connection") 302 | } 303 | 304 | endTag="" 305 | seek(imd,where=-2*nchar(endTag),origin="end") 306 | fileEndString=paste(readBin(imd, what="character", size=2, n=2*nchar(endTag), signed=FALSE),collapse="") 307 | 308 | if (fileEndString != endTag) { 309 | stop("The xml tail is either missing or irregular.") 310 | } 311 | 312 | #read in chunks until the beginning of the xml is reached 313 | chunkLength=1024 314 | seek(imd,where=-2*chunkLength,origin="current") 315 | xmlChunk=c() 316 | while (!(0 %in% xmlChunk)) { 317 | xmlChunk=c(readBin(imd, what="integer", size=2, n=chunkLength, signed=FALSE),xmlChunk) 318 | seek(imd,where=-4*chunkLength,origin="current") 319 | if (length(xmlChunk)>2^17) {stop("Didn't find zeros preceding xml.")} 320 | } 321 | # return to the position at which the xmlChunk begins 322 | seek(imd,where=2*chunkLength,origin="current") 323 | 324 | # convert to char and trim extra before the xml 325 | startTag="0) { 359 | slopeString=paste(slopeString,paste(rep("0",charDiff),sep="",collapse=""),sep="") 360 | } else if (charDiff<0) { slopeString=substr(slopeString,1,numChars) } 361 | 362 | newXml=sub(oldSlopes[i],slopeString,newXml,fixed=T) 363 | 364 | #make new intercept string same length as old intercept string 365 | numChars=nchar(oldIntercepts[i]) 366 | intString=as.character(averagedCoeffs["intercepts",i]) 367 | charDiff=numChars-nchar(intString) 368 | if (charDiff>0) { 369 | intString=paste(intString,paste(rep("0",charDiff),sep="",collapse=""),sep="") 370 | } else if (charDiff<0) { 371 | intString=substr(intString,1,numChars) 372 | } 373 | newXml=sub(oldIntercepts[i],intString,newXml,fixed=T) 374 | } 375 | 376 | # convert back to int and make new xmlChunk 377 | newXmlInt=utf8ToInt(newXml) 378 | if (length(newXmlInt) != (length(xmlChunk)-matchInd + 1)) { 379 | stop("New xml is not same length as old xml.") 380 | } 381 | xmlChunk[matchInd:length(xmlChunk)]=newXmlInt 382 | 383 | # overwrite the old xml with the new xml, given that the IMD file is still open at the same location 384 | writeBin(xmlChunk,imd,size=2) 385 | close(imd) 386 | cat(imdFile, " has been rewritten.") 387 | } 388 | 389 | cytofCore.copyImdXml = function(sourceImd,targetImd) { 390 | # Write an XML Tail on an IMD file that was truncated before the tail was written by copying it from another IMD file. 391 | # Note that the other IMD file MUST have the same panel and dual slopes for this to be accurate. 392 | # If you do not have another IMD file with the same panel and tail, create one with this panel. 393 | # If the dual slopes have been adjusted since the target file was acquired, it is possible to acquire in Dd mode and then rewrite the slopes with cytofCore.rewriteImdCoeffs 394 | 395 | # read XML from source IMD file and convert to integers 396 | sourceXml=cytofCore.read.imd.xml(sourceImd) 397 | imdInt=utf8ToInt(sourceXml$rawText) 398 | 399 | # write XML to target file 400 | imd <- file(targetImd, "ab") 401 | if (!isSeekable(imd)) { 402 | stop("Cannot seek in specified file or connection") 403 | } 404 | writeBin(imdInt,imd,size=2) 405 | close(imd) 406 | 407 | cat("XML from ",sourceImd, " has been appended to ",targetImd) 408 | } 409 | -------------------------------------------------------------------------------- /R/read.R: -------------------------------------------------------------------------------- 1 | cytofCore.read.conf <- function(file) { 2 | read.table(file,header=TRUE) 3 | } 4 | 5 | cytofCore.read.imd.xml <- function(file) { 6 | # file is the name of an IMD file 7 | # this function extracts the XML tail from the IMD file 8 | # returns a list with elements "analytes", "dualCalibration" and "rawText" 9 | # analytes is a data frame with columns of the mass, description and channel 10 | # dualCalibration is a data frame with columns of the dual mass, slope and intercept 11 | # rawText is a character string of the entire XML tail 12 | 13 | library("XML") 14 | 15 | # extract xml from tail of imd 16 | imd <- file(file, "rb") 17 | on.exit(close(imd)) 18 | if (!isSeekable(imd)) { 19 | stop("Cannot seek in specified file or connection") 20 | } 21 | 22 | endTag="" 23 | seek(imd,where=-2*nchar(endTag),origin="end") 24 | fileEndString=paste(readBin(imd, what="character", size=2, n=2*nchar(endTag), signed=FALSE),collapse="") 25 | 26 | if (fileEndString != endTag) { 27 | stop("The xml tail is either missing or irregular.") 28 | } 29 | 30 | #read in chunks until the beginning of the xml is reached 31 | chunkLength=1024 32 | seek(imd,where=-2*chunkLength,origin="current") 33 | xmlChunk=c() 34 | while (!(0 %in% xmlChunk)) { 35 | xmlChunk=c(readBin(imd, what="integer", size=2, n=chunkLength, signed=FALSE),xmlChunk) 36 | seek(imd,where=-4*chunkLength,origin="current") 37 | if (length(xmlChunk)>2^17) {stop("Didn't find zeros preceding xml.")} 38 | } 39 | 40 | # convert to char and trim extra before the xml 41 | startTag=" 0) { 129 | if (!isSeekable(file)) { 130 | stop("Cannot seek in specified file or connection") 131 | } 132 | # Each analyte consumes 4 bytes, 2 each for intensity and pulse values 133 | seek(file, where=start_push*num_analytes*4, origin="current") 134 | } 135 | 136 | # while (is.null(num_pushes) || current_push < num_pushes) { 137 | # desired_n <- ifelse(is.null(num_pushes), 2^16, num_pushes-current_push) * num_analytes * 2 138 | # if (exists("N")) { 139 | # before_n <- length(N) 140 | # N <- c(N,readBin(file, integer(), size=2, n=desired_n, signed=FALSE)) # Records are 16-bit unsigned integers 141 | # actual_n <- length(N)-before_n 142 | # } else { 143 | # N <- readBin(file, integer(), size=2, n=desired_n, signed=FALSE) # Records are 16-bit unsigned integers 144 | # actual_n <- length(N) 145 | # } 146 | # 147 | # if (actual_n < desired_n) { 148 | # break; 149 | # } 150 | # current_push <- as.integer(length(N) / num_analytes / 2) 151 | # } 152 | 153 | #simplifying: just read in num_pushes number of pushes 154 | N=readBin(file,integer(),size=2,n=num_pushes*2*num_analytes,signed=F) 155 | 156 | I_cols <- seq(from=1, by=2, length.out=num_analytes) 157 | P_cols <- seq(from=2, by=2, length.out=num_analytes) 158 | IP <- matrix(N,ncol=2*num_analytes,byrow=TRUE) 159 | 160 | # 20140709 updated dual conditions to those used by CyTOF software 161 | D <- c() 162 | for (i in 1:num_analytes) { 163 | d <- round(IP[,I_cols[i]]*slopes[i]+intercepts[i]) 164 | use_pulse = d < IP[,P_cols[i]] & IP[,P_cols[i]]<= pulse_thresh 165 | d[use_pulse] <- IP[use_pulse,P_cols[i]] 166 | D <- cbind(D, d) 167 | } 168 | colnames(D) <- analytes 169 | 170 | # Changing from earlier version and calculating I and P even if conf supplied 171 | l <- list(intensity=IP[,I_cols],pulse=IP[,P_cols],dual=D) 172 | colnames(l$intensity) <- analytes 173 | colnames(l$pulse) <- analytes 174 | 175 | return(l) 176 | } 177 | 178 | cytofCore.read.rd8.cytof1 <- function(file, segmentSize=NULL, massCalibration=NULL, start_push=0, num_pushes=2^8) { 179 | #returns a list with raw intensities where each row is a push and each column is the tof trace of that push. 180 | #optionally returns which column corresponds to which mass 181 | #segmentSize defaults to 3200 if not specified but if this is incorrect the results won't make sense 182 | #including the optional input argument of the massCalibration adds the massPeak locations to the list 183 | #the massCalibration parameter is a list with names "time", "mass", and "triggerDelay". 184 | #"time" and "mass" are 2-element vectors whose values are visible in the CyTOF software mass calibration window 185 | # Example: massCalibration=list(mass=c(132.905,192.963),time=c(9597,11537),triggerDelay=8416) 186 | 187 | if (is.character(file)) { 188 | file <- file(file, "rb") 189 | on.exit(close(file)) 190 | } 191 | 192 | results=list() 193 | 194 | # cytof1 has 1 uint8 value per intensity sample 195 | 196 | if(is.null(segmentSize)) { 197 | segmentSize=3200 } 198 | seek(file, where=start_push*segmentSize, origin="start") 199 | N=readBin(file,integer(),size=1,n=num_pushes*segmentSize,signed=F) 200 | intensity <- matrix(N,ncol=segmentSize,byrow=TRUE,dimnames=list(as.character(start_push:(start_push+num_pushes-1)))) 201 | 202 | results$intensity=intensity 203 | 204 | #calibrate the mass windows to the raw data 205 | if (!is.null(massCalibration)) { 206 | A=(massCalibration$time[1]-massCalibration$time[2])/(sqrt(massCalibration$mass[1]) - sqrt(massCalibration$mass[2])) 207 | T0=massCalibration$time[1]-A*sqrt(massCalibration$mass[1]) 208 | masses=102:195 209 | massPeaks=T0+A*sqrt(masses) - massCalibration$triggerDelay; 210 | names(massPeaks)=as.character(masses) 211 | 212 | # the mass peaks correspond to the columns of the intensities 213 | results$massPeaks=massPeaks 214 | } 215 | 216 | return(results) 217 | 218 | } 219 | 220 | cytofCore.read.rd8.cytof2 <- function(file, referenceFCS, start_push=0, num_pushes=2^8) { 221 | #returns a list with two tables of raw intensities, where each row is a push and each column is the tof trace of that push. 222 | #also returns which column corresponds to which mass 223 | #the mass calibration values are read in from the xml after the data segment in a cytof2 fcs file acquired with the same settings as the rd8 224 | 225 | if (is.character(file)) { 226 | file <- file(file, "rb") 227 | on.exit(close(file)) 228 | } 229 | 230 | results=list() 231 | 232 | # read segment size, trigger delay, A and T0 from an fcs file aquired with the same settings 233 | tofCalibration=cytofCore.read.tof.calibration(referenceFCS) 234 | segmentSize=tofCalibration$segmentSize 235 | # cytof2 has 2 uint8 values for each sample 236 | 237 | 238 | seek(file, where=start_push*segmentSize*2, origin="current") 239 | N=readBin(file,integer(),size=1,n=num_pushes*segmentSize*2,signed=F) 240 | board1_cols <- seq(from=1, by=2, length.out=segmentSize) 241 | board2_cols <- seq(from=2, by=2, length.out=segmentSize) 242 | bothBoards <- matrix(N,ncol=2*segmentSize,byrow=TRUE,dimnames=list(as.character(start_push:(start_push+num_pushes-1)))) 243 | intensity=list(board1=bothBoards[,board1_cols], board2=bothBoards[,board2_cols] ) 244 | 245 | 246 | results$intensity=intensity 247 | 248 | #calibrate the mass windows to the raw data 249 | 250 | masses=89:195 251 | massPeaks=tofCalibration$T0+tofCalibration$A*sqrt(masses) - tofCalibration$triggerDelay; 252 | names(massPeaks)=as.character(masses) 253 | 254 | # the mass peaks correspond to the columns of the intensities 255 | results$massPeaks=massPeaks 256 | 257 | return(results) 258 | 259 | } 260 | 261 | cytofCore.read.tof.calibration <- function(filename) { 262 | # finds the segment size, trigger delay, A and T0 from the xml written after the data segment of a Cytof2 fcs file 263 | 264 | if (is.character(file)) { 265 | file <- file(filename, "rb") 266 | on.exit(close(file)) 267 | } 268 | 269 | seek(file, where=10, origin="start") 270 | headerStartPos=as.integer(intToUtf8(readBin(file,"integer",n=8,size=1,signed=FALSE))) 271 | headerStopPos=as.integer(intToUtf8(readBin(file,"integer",n=8,size=1,signed=FALSE))) 272 | 273 | seek(file, where=headerStartPos,origin="start") 274 | fcsHeader=intToUtf8(readBin(file,"integer",n=headerStopPos-headerStartPos+1,size=1,signed=FALSE)) 275 | delimiter=substr(fcsHeader,1,1) 276 | 277 | # parsing of header to get enddata position 278 | pattern=paste0(".*",delimiter,"\\$ENDDATA",delimiter,"(\\d+)",delimiter,".*") 279 | endPos=sub(pattern,"\\1",fcsHeader) 280 | 281 | # move to position just after end of data 282 | seek(file,where=as.integer(endPos)+1,origin="start") 283 | 284 | #read in chunks until the end of the xml is reached 285 | chunkLength=1024 286 | xmlChunk=intToUtf8(readBin(file,what="integer",size=1,n=2*chunkLength,signed=F)) 287 | while (length(grep("",substr(xmlChunk,nchar(xmlChunk)-2*chunkLength+1,nchar(xmlChunk))))==0) { 288 | xmlChunk=paste0(xmlChunk,intToUtf8(readBin(file, what="integer", size=1, n=chunkLength, signed=FALSE))) 289 | if (nchar(xmlChunk)>2^17) {stop("Didn't find end of xml.")} 290 | } 291 | 292 | # trim to just the xml 293 | xml=sub("(.*).*","\\1",xmlChunk) 294 | 295 | result=list() 296 | 297 | # extract the tof calibration values from the xml 298 | xmlList=xmlToList(xml) 299 | acquisitionBoardParams=xmlList[["Acquisition"]][["AcquisitionBoardParams"]] 300 | boardList=xmlToList(acquisitionBoardParams) 301 | result$triggerDelay=as.integer(boardList[["Params"]][["TriggerDelay"]]) 302 | result$segmentSize=as.integer(boardList[["Params"]][["SegmentSize"]]) 303 | result$A=as.numeric(xmlList[["CalibrationResults"]][["A"]]) 304 | result$T0=as.numeric(xmlList[["CalibrationResults"]][["T0"]]) 305 | 306 | return(result) 307 | } -------------------------------------------------------------------------------- /R/write.R: -------------------------------------------------------------------------------- 1 | cytofCore.write.FCS <- function(x, filename, what="numeric",channelDescriptions=NULL,referenceDescription=NULL, oldDescription=NULL) { 2 | if (is.matrix(x)) { 3 | # Don't write "Leading_Push" to FCS files 4 | x <- x[,which(colnames(x) != "Leading_Push")] 5 | 6 | # Build metadata for FCS file 7 | pd <- c() # 'params' phenoData 8 | dl <- list() # 'description' list 9 | 10 | dl[["$DATATYPE"]] <- "F" 11 | 12 | if (!is.null(referenceDescription)) { 13 | if (!is.null(referenceDescription[["$DATE"]])){ 14 | dl[["$DATE"]] <- referenceDescription[["$DATE"]] 15 | } 16 | if (!is.null(referenceDescription[["$BTIM"]])){ 17 | dl[["$BTIM"]] <- referenceDescription[["$BTIM"]] 18 | } 19 | if (!is.null(referenceDescription[["$ETIM"]])){ 20 | dl[["$ETIM"]] <- referenceDescription[["$ETIM"]] 21 | } 22 | if (!is.null(referenceDescription[["$CYT"]])){ 23 | dl[["$CYT"]] <- referenceDescription[["$CYT"]] 24 | } 25 | if (!is.null(referenceDescription[["$CYTSN"]])){ 26 | dl[["$CYTSN"]] <- referenceDescription[["$CYTSN"]] 27 | } 28 | 29 | } 30 | 31 | for (c in 1:ncol(x)) { 32 | c_name <- colnames(x)[c] 33 | c_desc <- colnames(x)[c] 34 | if (!is.null(channelDescriptions)){ 35 | if (!is.na(channelDescriptions[c])){ 36 | c_desc <- channelDescriptions[c] 37 | } 38 | } 39 | 40 | c_min <- floor(min(0,min(x[,c]))) # Hack to prevent flowCore from shifting range 41 | c_max <- ceiling(max(x[,c])) 42 | c_rng <- c_max - c_min + 1 43 | 44 | pl <- matrix(c(c_name, c_desc, c_rng, c_min, c_max),nrow=1) 45 | colnames(pl) <- c("name", "desc", "range", "minRange", "maxRange") 46 | rownames(pl) <- paste("$P",c,sep="") 47 | pd <- rbind(pd, pl) 48 | 49 | if (!is.null(referenceDescription[[paste0("P",c,"DISPLAY")]])){ 50 | dl[[paste0("P",c,"DISPLAY")]] <- referenceDescription[[paste0("P",c,"DISPLAY")]] 51 | } 52 | 53 | if (!is.null(referenceDescription[[paste0("$P",c,"G")]])){ 54 | dl[[paste0("$P",c,"G")]] <- referenceDescription[[paste0("$P",c,"G")]] 55 | } 56 | 57 | if (!is.null(referenceDescription[[paste0("$P",c,"R")]])){ 58 | dl[[paste0("$P",c,"R")]] <- referenceDescription[[paste0("$P",c,"R")]] 59 | } else { 60 | dl[[paste("$P",c,"R",sep="")]] <- toString(c_rng); # Range 61 | } 62 | 63 | if (!is.null(referenceDescription[[paste0("$P",c,"B")]])){ 64 | dl[[paste0("$P",c,"B")]] <- referenceDescription[[paste0("$P",c,"B")]] 65 | } else { 66 | dl[[paste("$P",c,"B",sep="")]] <- "32"; # Number of bits 67 | } 68 | 69 | if (!is.null(referenceDescription[[paste0("$P",c,"E")]])){ 70 | dl[[paste0("$P",c,"E")]] <- referenceDescription[[paste0("$P",c,"E")]] 71 | } else { 72 | dl[[paste("$P",c,"E",sep="")]] <- "0,0"; # Exponent 73 | } 74 | 75 | dl[[paste("$P",c,"N",sep="")]] <- c_name; # Name 76 | dl[[paste("$P",c,"S",sep="")]] <- c_desc; # Desc 77 | } 78 | 79 | 80 | if (!is.null(oldDescription)) { 81 | if (!is.null(oldDescription[["$CYT"]])){ 82 | dl[["$CYT"]] <- oldDescription[["$CYT"]] 83 | } 84 | if (!is.null(oldDescription[["$DATE"]])){ 85 | dl[["$DATE"]] <- oldDescription[["$DATE"]] 86 | } 87 | if (!is.null(oldDescription[["$BTIM"]])){ 88 | dl[["$BTIM"]] <- oldDescription[["$BTIM"]] 89 | } 90 | if (!is.null(oldDescription[["$ETIM"]])){ 91 | dl[["$ETIM"]] <- oldDescription[["$ETIM"]] 92 | } 93 | } 94 | 95 | x <- flowFrame(x, as(data.frame(pd), "AnnotatedDataFrame"), description=dl) 96 | } 97 | write.FCS(x, filename, what) 98 | } 99 | 100 | cytofCore.write.IMD.stream = function(imdFile,confFile,windowSize=10000,startTime=0,endTime=NULL){ 101 | 102 | timeConstant = 1/76800 103 | continue=T 104 | counter=0; 105 | first=T 106 | 107 | #FILL THIS OUT 108 | num_pushes <- as.integer(file.info(imdFile)$size / nrow(cytofCore.read.conf(confFile)) / 4) 109 | max_time = (num_pushes-1)*timeConstant*1000 110 | if (startTime>max_time){ 111 | stop(paste("Specified startTime is greater than IMD max time of",max_time)) 112 | } 113 | if (!is.null(endTime)&&(endTime>max_time)){ 114 | stop(paste("Specified endTime is greater than IMD max time of",max_time,". Leave endTime as NULL (default) to read to end of file.")) 115 | } 116 | 117 | while (continue){ 118 | windowStartTime = (counter)*(windowSize)*timeConstant*1000 119 | windowEndTime = (counter*windowSize+windowSize-1)*timeConstant*1000 120 | windowTime = seq(from=windowStartTime,to=windowEndTime,by=timeConstant*1000) 121 | #print(paste(windowStartTime,windowEndTime)) 122 | windowKeep=F 123 | if (any(windowTime>=startTime)){ 124 | windowKeep = windowTime>=startTime 125 | } 126 | 127 | if (!is.null(endTime)){ 128 | windowKeep = windowKeep & (windowTime<=endTime) 129 | if (windowStartTime>endTime){ 130 | continue=F 131 | } 132 | } 133 | 134 | 135 | if (sum(windowKeep)>0){ 136 | startPush=counter*windowSize 137 | if ((startPush+windowSize)>num_pushes){ 138 | pushes=cytofCore.read.imd(file=imdFile,conf=confFile,start_push=startPush)$dual 139 | windowTime = windowTime[1:nrow(pushes)] 140 | windowKeep = windowKeep[1:nrow(pushes)] 141 | continue=F 142 | } else { 143 | pushes = cytofCore.read.imd(file=imdFile,conf=confFile,start_push=startPush,num_pushes=windowSize)$dual 144 | } 145 | pushes = cbind(time=sprintf("%.3f",windowTime[windowKeep]),pushes[windowKeep,]) 146 | print(paste("Writing",nrow(pushes),"pushes")) 147 | if (first){ 148 | write.table(pushes,file=paste(imdFile,".txt",sep=""),quote=F,row.names=F,col.names=T,append=F) 149 | first=F 150 | } else { 151 | write.table(pushes,file=paste(imdFile,".txt",sep=""),quote=F,row.names=F,col.names=F,append=T) 152 | } 153 | } 154 | 155 | counter=counter+1; 156 | 157 | } 158 | } 159 | -------------------------------------------------------------------------------- /README.mediawiki: -------------------------------------------------------------------------------- 1 | ==CyTOFCore README 0.3== 2 | ===Installation=== 3 | The cytofCore package can be installed directly from github using the devtools package. Start R and run the following commands: 4 | R>install.packages("devtools") 5 | R>install.packages("XML") 6 | R>library("devtools") 7 | You will need to install flowCore if you have not already: 8 | R>source("http://bioconductor.org/biocLite.R") 9 | R>biocLite("flowCore") 10 | Now install the cytofCore package 11 | R>install_github("nolanlab/cytofCore") 12 | 13 | ===Editing the Panel of a set of FCS Files=== 14 | The cytofCore.updatePanel function can be used to edit the panel written into the header of a set of FCS files. Typical edits include making spelling consistent (e.g., HLADR vs. HLA-DR), removing entire columns, re-ordering columns, etc. To use the panel editor, you must first prepare a template file with the desired panel. It can take one of two forms: 15 | 16 | *FCS Template: You may use an existing FCS file that has the correct panel as your template. 17 | 18 | *Spreadsheet Template: You may write your desired panel into a spreadsheet. The first column should be a list of the channel names, and the second column should be the marker you want to write into those channels. You must save your spreadsheet as a CSV or tab-delimited TXT file. Below is an example spreadsheet that would create FCS files with only four parameters 19 | 20 | {| class="wikitable" style="margin: auto;" 21 | |- 22 | | Time 23 | | Time 24 | |- 25 | | Cell_length 26 | | Cell_length 27 | |- 28 | | (Ir191)Di 29 | | DNA1 30 | |- 31 | | (Ir193)Di 32 | | DNA2 33 | |} 34 | 35 | You must put all the FCS files whose panels you want to update to the template's panel into a single folder. 36 | 37 | In every FCS file in the selected folder, the panel updater will search for each metal listed in the template, and then will write that metal's marker as it is written in the template. It will put the list of metals/markers in the same order in each file. If a metal is not found, it will ask whether you want to include a placeholder column of zeros, or if you want to omit that channel from that file. A subfolder called 'relabeled' will be created within the selected folder, and new FCS files will be written there. 38 | 39 | To use the panel editor, you must load the cytofCore library, and then call the cytofCore.updatePanel function: 40 | 41 | R>library("cytofCore") 42 | R>cytofCore.updatePanel() 43 | 44 | This will prompt you to choose the template file, and then the folder of FCS files. When choosing the folder, you must actually enter into that folder in the selection window before clicking OK. 45 | 46 | You can also specify the folder and/or template directly: 47 | 48 | R>cytofCore.updatePanel(templateFile="/path/to/templatefile", fcsFolder="/path/to/files/to/fix/") 49 | 50 | ===Adding the XML tail (or "header") to an IMD File=== 51 | In the occasional circumstance that the CyTOF software crashes or is forced to quit while still writing an IMD file, the XML tail of the IMD file that includes the panel and dual calibration information may not get written. It is necessary to add this information to the IMD file before extracting the cell events. If you attempt to convert the IMD file to an FCS file without this, you will get a warning from the CyTOF software along the lines of "missing header." (While this is commonly called the "header," it is actually at the tail of the file.) You will also see no channels if you click "Select Channels" in the IMD analysis window. The easiest way to fix this is to copy the entire XML tail from another IMD file that has the same panel and dual calibration values. To do this: 52 | 53 | R>library("cytofCore") 54 | R>cytofCore.copyImdXml(sourceImdFilename,targetImdFilename) 55 | 56 | For example, if the name of the truncated file is ''fileWithoutXml.imd'', and the name of the template file is ''fileWithXml.imd'', the command would be 57 | 58 | R>cytofCore.copyImdXml("fileWithXml.imd","fileWithoutXml.imd") 59 | 60 | It is strongly recommended to apply this code only to files that have been backed up. 61 | 62 | Note that you either need to use a full path to the file, or change your working directory using setwd: 63 | 64 | R>setwd("/path/to/directory/with/imdfiles") 65 | 66 | 79 | 80 | 92 | -------------------------------------------------------------------------------- /cytofCore.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | BuildType: Package 16 | PackageInstallArgs: --no-multiarch --with-keep.source 17 | -------------------------------------------------------------------------------- /inst/automator/R/ExtractIMD.R: -------------------------------------------------------------------------------- 1 | library("cytofCore") 2 | args = commandArgs() 3 | print(args) 4 | if (sum(grep("imd$",args))<1 || sum(grep("conf$",args))<1){ 5 | stop("Can't find IMD or Conf missing") 6 | } 7 | imdFile = args[grep("imd$",args)] 8 | confFile = args[grep("conf$",args)] 9 | startTime = as.numeric(args[5]) 10 | endTime=as.numeric(args[6]) 11 | if (endTime=="EndOfFile"){ 12 | endTime=NULL 13 | } else { 14 | endTime=as.numeric(endTime) 15 | } 16 | print(paste("Extracting from",startTime,"to",endTime)); 17 | cytofCore.write.IMD.stream(imdFile=imdFile,confFile=confFile,startTime=startTime,endTime=endTime) 18 | 19 | -------------------------------------------------------------------------------- /inst/automator/R/Subtract100.R: -------------------------------------------------------------------------------- 1 | library("cytofCore") 2 | args = commandArgs(); 3 | for (filename in args){ 4 | if (sum(grep(".fcs",filename,ignore.case=T))==0){ 5 | cat(paste("Ignoring argument",filename,"\n")) 6 | } else { 7 | cat(paste("Subtracting from ",filename,".\n",sep="")) 8 | outputFile = write.FCS(cytofCore.subtract(flowFrame=read.FCS(filename),value=100),filename=paste(filename,".subtracted.fcs",sep="")) 9 | cat(paste("Output File: ",outputFile,".\n\n",sep="")) 10 | } 11 | } -------------------------------------------------------------------------------- /inst/automator/apps/Concatenate.app/Contents/Info.plist: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | AMIsApplet 6 | 7 | AMStayOpen 8 | 9 | BuildMachineOSBuild 10 | 12C32 11 | CFBundleDevelopmentRegion 12 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Automator 313 | 314 | AMParameterProperties 315 | 316 | COMMAND_STRING 317 | 318 | CheckedForUserDefaultShell 319 | 320 | inputMethod 321 | 322 | shell 323 | 324 | source 325 | 326 | 327 | AMProvides 328 | 329 | Container 330 | List 331 | Types 332 | 333 | com.apple.cocoa.string 334 | 335 | 336 | ActionBundlePath 337 | /System/Library/Automator/Run Shell Script.action 338 | ActionName 339 | Run Shell Script 340 | ActionParameters 341 | 342 | COMMAND_STRING 343 | /usr/bin/R --no-save $@ << RSCRIPT 344 | ####### BEGIN Subtract100.R 345 | library("cytofCore") 346 | files = commandArgs() 347 | files = files[grep(".fcs",files)] 348 | cytofCore.concatenateFiles(files) 349 | RSCRIPT 350 | CheckedForUserDefaultShell 351 | 352 | inputMethod 353 | 1 354 | shell 355 | /bin/bash 356 | source 357 | 358 | 359 | BundleIdentifier 360 | com.apple.RunShellScript 361 | CFBundleVersion 362 | 2.0.3 363 | CanShowSelectedItemsWhenRun 364 | 365 | CanShowWhenRun 366 | 367 | Category 368 | 369 | AMCategoryUtilities 370 | 371 | Class Name 372 | RunShellScriptAction 373 | Disabled 374 | 375 | InputUUID 376 | BDE39688-E006-40FC-90E8-DF91B39C2FBD 377 | Keywords 378 | 379 | Shell 380 | Script 381 | Command 382 | Run 383 | Unix 384 | 385 | OutputUUID 386 | 2492FF4C-B481-4485-A13C-F38025E64529 387 | ShowWhenRun 388 | 389 | UUID 390 | 9DB6D5EC-732B-4423-A6D9-F2A0E2AFBC2C 391 | UnlocalizedApplications 392 | 393 | Automator 394 | 395 | arguments 396 | 397 | 0 398 | 399 | default value 400 | 0 401 | name 402 | inputMethod 403 | required 404 | 0 405 | type 406 | 0 407 | uuid 408 | 0 409 | 410 | 1 411 | 412 | default value 413 | 414 | name 415 | source 416 | required 417 | 0 418 | type 419 | 0 420 | uuid 421 | 1 422 | 423 | 2 424 | 425 | default value 426 | 427 | name 428 | CheckedForUserDefaultShell 429 | required 430 | 0 431 | type 432 | 0 433 | uuid 434 | 2 435 | 436 | 3 437 | 438 | default value 439 | 440 | name 441 | COMMAND_STRING 442 | required 443 | 0 444 | type 445 | 0 446 | uuid 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ActionName 50 | Get Specified Finder Items 51 | ActionParameters 52 | 53 | fileNames 54 | 55 | ~/Desktop/notime/tc/CMP.fcs 56 | ~/Desktop/notime/tc/Erythroblast.fcs 57 | ~/Desktop/notime/tc/GMP.fcs 58 | 59 | 60 | BundleIdentifier 61 | com.apple.Automator.SpecifiedFiles 62 | CFBundleVersion 63 | 1.1.1 64 | CanShowSelectedItemsWhenRun 65 | 66 | CanShowWhenRun 67 | 68 | Category 69 | 70 | AMCategoryFilesAndFolders 71 | 72 | Class Name 73 | SpecifiedFilesAction 74 | Disabled 75 | 76 | InputUUID 77 | E9A7B547-5201-4E46-B5EB-8BE33B2C657F 78 | Keywords 79 | 80 | File 81 | Choose 82 | Find 83 | Get 84 | 85 | OutputUUID 86 | 5599059A-CF27-4866-BF97-5AD86810D43C 87 | ShowWhenRun 88 | 89 | UUID 90 | 61E1656B-0856-49B3-AC0B-658A9094872E 91 | UnlocalizedApplications 92 | 93 | Finder 94 | 95 | arguments 96 | 97 | 0 98 | 99 | default value 100 | 101 | name 102 | fileNames 103 | required 104 | 0 105 | type 106 | 0 107 | uuid 108 | 0 109 | 110 | 111 | isViewVisible 112 | 113 | location 114 | 619.500000:901.000000 115 | nibPath 116 | /System/Library/Automator/Get Specified Finder Items.action/Contents/Resources/English.lproj/main.nib 117 | 118 | isViewVisible 119 | 120 | 121 | 122 | action 123 | 124 | AMAccepts 125 | 126 | Container 127 | List 128 | Optional 129 | 130 | Types 131 | 132 | 133 | AMActionVersion 134 | 1.0.1 135 | AMApplication 136 | 137 | Automator 138 | 139 | AMParameterProperties 140 | 141 | affirmativeTitle 142 | 143 | displayWarning 144 | 145 | explanationText 146 | 147 | negativeTitle 148 | 149 | questionText 150 | 151 | tokenizedValue 152 | 153 | CyTOF Core Message: 154 | 155 | 156 | 157 | AMProvides 158 | 159 | Container 160 | List 161 | Types 162 | 163 | 164 | ActionBundlePath 165 | /System/Library/Automator/Ask for Confirmation.action 166 | ActionName 167 | Ask for Confirmation 168 | ActionParameters 169 | 170 | affirmativeTitle 171 | OK 172 | displayWarning 173 | 174 | explanationText 175 | Drag an FCS file on to the Subtract100.app to subtract 100 from parameters. The first two columns are excluded by default. 176 | 177 | Subtraction will run in background and a text file with output will appear when complete. 178 | 179 | IMPORTANT: File names may not have spaces anywhere in their paths. 180 | negativeTitle 181 | Cancel 182 | questionText 183 | CyTOF Core Message: 184 | 185 | BundleIdentifier 186 | com.apple.Automator.Ask for Confirmation 187 | CFBundleVersion 188 | 1.0.1 189 | CanShowSelectedItemsWhenRun 190 | 191 | CanShowWhenRun 192 | 193 | Category 194 | 195 | AMCategoryUtilities 196 | 197 | Class Name 198 | AMAskForConfirmationAction 199 | InputUUID 200 | 7A60EE39-0B87-466D-A673-21585425891A 201 | Keywords 202 | 203 | Message 204 | Ask 205 | Display 206 | Prompt 207 | Show 208 | 209 | OutputUUID 210 | BDBBA9AB-2C26-46F1-A52E-7A3D3B49983F 211 | UUID 212 | 53AC3122-7423-461A-83F1-D9F619232F19 213 | UnlocalizedApplications 214 | 215 | Automator 216 | 217 | arguments 218 | 219 | 0 220 | 221 | default value 222 | 223 | name 224 | questionText 225 | required 226 | 0 227 | type 228 | 0 229 | uuid 230 | 0 231 | 232 | 1 233 | 234 | default value 235 | 236 | name 237 | displayWarning 238 | required 239 | 0 240 | type 241 | 0 242 | uuid 243 | 1 244 | 245 | 2 246 | 247 | default value 248 | 249 | name 250 | explanationText 251 | required 252 | 0 253 | type 254 | 0 255 | uuid 256 | 2 257 | 258 | 3 259 | 260 | default value 261 | OK 262 | name 263 | affirmativeTitle 264 | required 265 | 0 266 | type 267 | 0 268 | uuid 269 | 3 270 | 271 | 4 272 | 273 | default value 274 | Cancel 275 | name 276 | negativeTitle 277 | required 278 | 0 279 | type 280 | 0 281 | uuid 282 | 4 283 | 284 | 285 | isViewVisible 286 | 287 | location 288 | 619.500000:663.000000 289 | nibPath 290 | /System/Library/Automator/Ask for Confirmation.action/Contents/Resources/English.lproj/main.nib 291 | 292 | isViewVisible 293 | 294 | 295 | 296 | action 297 | 298 | AMAccepts 299 | 300 | Container 301 | List 302 | Optional 303 | 304 | Types 305 | 306 | com.apple.cocoa.string 307 | 308 | 309 | AMActionVersion 310 | 2.0.2 311 | AMApplication 312 | 313 | Automator 314 | 315 | AMParameterProperties 316 | 317 | COMMAND_STRING 318 | 319 | CheckedForUserDefaultShell 320 | 321 | inputMethod 322 | 323 | shell 324 | 325 | source 326 | 327 | 328 | AMProvides 329 | 330 | Container 331 | List 332 | Types 333 | 334 | com.apple.cocoa.string 335 | 336 | 337 | ActionBundlePath 338 | /System/Library/Automator/Run Shell Script.action 339 | ActionName 340 | Run Shell Script 341 | ActionParameters 342 | 343 | COMMAND_STRING 344 | /usr/bin/R --no-save $@ << RSCRIPT 345 | ####### BEGIN Subtract100.R 346 | library("cytofCore") 347 | args = commandArgs(); 348 | for (filename in args){ 349 | if (sum(grep(".fcs",filename,ignore.case=T))==0){ 350 | cat(paste("Ignoring argument",filename,"\n")) 351 | } else { 352 | cat(paste("Subtracting from ",filename,".\n",sep="")) 353 | outputFile = write.FCS(cytofCore.subtract(flowFrame=read.FCS(filename),value=100),filename=paste(filename,".subtracted.fcs",sep="")) 354 | cat(paste("Output File: ",outputFile,".\n\n",sep="")) 355 | } 356 | } 357 | ###### END Subtract100.R 358 | RSCRIPT 359 | 360 | CheckedForUserDefaultShell 361 | 362 | inputMethod 363 | 1 364 | shell 365 | /bin/bash 366 | source 367 | 368 | 369 | BundleIdentifier 370 | com.apple.RunShellScript 371 | CFBundleVersion 372 | 2.0.2 373 | CanShowSelectedItemsWhenRun 374 | 375 | CanShowWhenRun 376 | 377 | Category 378 | 379 | AMCategoryUtilities 380 | 381 | Class Name 382 | RunShellScriptAction 383 | Disabled 384 | 385 | InputUUID 386 | BDE39688-E006-40FC-90E8-DF91B39C2FBD 387 | Keywords 388 | 389 | Shell 390 | Script 391 | Command 392 | Run 393 | Unix 394 | 395 | OutputUUID 396 | 2492FF4C-B481-4485-A13C-F38025E64529 397 | ShowWhenRun 398 | 399 | UUID 400 | 9DB6D5EC-732B-4423-A6D9-F2A0E2AFBC2C 401 | UnlocalizedApplications 402 | 403 | Automator 404 | 405 | arguments 406 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490 | Optional 491 | 492 | Types 493 | 494 | com.apple.cocoa.attributed-string 495 | com.apple.cocoa.string 496 | 497 | 498 | AMActionVersion 499 | 1.2 500 | AMApplication 501 | 502 | TextEdit 503 | 504 | AMParameterProperties 505 | 506 | AMProvides 507 | 508 | Container 509 | List 510 | Types 511 | 512 | com.apple.textedit.document-object 513 | 514 | 515 | ActionBundlePath 516 | /System/Library/Automator/New TextEdit Document.action 517 | ActionName 518 | New TextEdit Document 519 | ActionParameters 520 | 521 | BundleIdentifier 522 | com.apple.Automator.CreateNewTextEditDocument 523 | CFBundleVersion 524 | 1.2 525 | CanShowSelectedItemsWhenRun 526 | 527 | CanShowWhenRun 528 | 529 | Category 530 | 531 | AMCategoryText 532 | 533 | Class Name 534 | AMNewTextEditDocumentAction 535 | InputUUID 536 | D1FA329F-02D1-4A77-A920-7F47FE5A6168 537 | Keywords 538 | 539 | Create 540 | Make 541 | Document 542 | Text 543 | New 544 | Display 545 | Open 546 | 547 | OutputUUID 548 | D4D8FE94-B474-44C8-9733-4EF8086125F7 549 | UUID 550 | 3CD32591-AACD-4493-9DDB-830DAF9DA47E 551 | UnlocalizedApplications 552 | 553 | TextEdit 554 | 555 | arguments 556 | 557 | 558 | 559 | 560 | action 561 | 562 | AMAccepts 563 | 564 | Container 565 | List 566 | Optional 567 | 568 | Types 569 | 570 | 571 | AMActionVersion 572 | 1.0.1 573 | AMApplication 574 | 575 | Automator 576 | 577 | AMParameterProperties 578 | 579 | affirmativeTitle 580 | 581 | displayWarning 582 | 583 | explanationText 584 | 585 | negativeTitle 586 | 587 | questionText 588 | 589 | tokenizedValue 590 | 591 | CyTOF Core Message: 592 | 593 | 594 | 595 | AMProvides 596 | 597 | Container 598 | List 599 | Types 600 | 601 | 602 | ActionBundlePath 603 | /System/Library/Automator/Ask for Confirmation.action 604 | ActionName 605 | Ask for Confirmation 606 | ActionParameters 607 | 608 | affirmativeTitle 609 | OK 610 | displayWarning 611 | 612 | explanationText 613 | Subtraction is Complete 614 | negativeTitle 615 | Cancel 616 | questionText 617 | CyTOF Core Message: 618 | 619 | BundleIdentifier 620 | com.apple.Automator.Ask for Confirmation 621 | CFBundleVersion 622 | 1.0.1 623 | CanShowSelectedItemsWhenRun 624 | 625 | CanShowWhenRun 626 | 627 | Category 628 | 629 | AMCategoryUtilities 630 | 631 | Class Name 632 | AMAskForConfirmationAction 633 | InputUUID 634 | 94DF18C2-7B64-414A-833B-3F3B9941561B 635 | Keywords 636 | 637 | Message 638 | Ask 639 | Display 640 | Prompt 641 | Show 642 | 643 | OutputUUID 644 | 7D9EE8DD-32F6-49E2-9895-2EFD325225C7 645 | UUID 646 | 51F52F42-C97B-4B3A-8DEC-5879154D2B70 647 | UnlocalizedApplications 648 | 649 | Automator 650 | 651 | arguments 652 | 653 | 0 654 | 655 | default value 656 | 657 | name 658 | questionText 659 | required 660 | 0 661 | type 662 | 0 663 | uuid 664 | 0 665 | 666 | 1 667 | 668 | default value 669 | 670 | name 671 | displayWarning 672 | required 673 | 0 674 | type 675 | 0 676 | uuid 677 | 1 678 | 679 | 2 680 | 681 | default value 682 | 683 | name 684 | explanationText 685 | required 686 | 0 687 | type 688 | 0 689 | uuid 690 | 2 691 | 692 | 3 693 | 694 | default value 695 | OK 696 | name 697 | affirmativeTitle 698 | required 699 | 0 700 | type 701 | 0 702 | uuid 703 | 3 704 | 705 | 4 706 | 707 | default value 708 | Cancel 709 | name 710 | negativeTitle 711 | required 712 | 0 713 | type 714 | 0 715 | uuid 716 | 4 717 | 718 | 719 | isViewVisible 720 | 721 | location 722 | 619.500000:217.000000 723 | nibPath 724 | /System/Library/Automator/Ask for Confirmation.action/Contents/Resources/English.lproj/main.nib 725 | 726 | isViewVisible 727 | 728 | 729 | 730 | connectors 731 | 732 | 48E66245-84AA-41F8-8A41-AF316632FD46 733 | 734 | from 735 | 9DB6D5EC-732B-4423-A6D9-F2A0E2AFBC2C - 9DB6D5EC-732B-4423-A6D9-F2A0E2AFBC2C 736 | to 737 | 3CD32591-AACD-4493-9DDB-830DAF9DA47E - 3CD32591-AACD-4493-9DDB-830DAF9DA47E 738 | 739 | 8DFFD017-F1AF-4E13-AD40-0586D8DE5382 740 | 741 | from 742 | 53AC3122-7423-461A-83F1-D9F619232F19 - 53AC3122-7423-461A-83F1-D9F619232F19 743 | to 744 | 9DB6D5EC-732B-4423-A6D9-F2A0E2AFBC2C - 9DB6D5EC-732B-4423-A6D9-F2A0E2AFBC2C 745 | 746 | ED21FFB2-A333-48C9-B23F-80CE12E2A6BE 747 | 748 | from 749 | 61E1656B-0856-49B3-AC0B-658A9094872E - 61E1656B-0856-49B3-AC0B-658A9094872E 750 | to 751 | 53AC3122-7423-461A-83F1-D9F619232F19 - 53AC3122-7423-461A-83F1-D9F619232F19 752 | 753 | F42CF6C2-5777-46EB-9BE4-47C4C3928CB9 754 | 755 | from 756 | 3CD32591-AACD-4493-9DDB-830DAF9DA47E - 3CD32591-AACD-4493-9DDB-830DAF9DA47E 757 | to 758 | 51F52F42-C97B-4B3A-8DEC-5879154D2B70 - 51F52F42-C97B-4B3A-8DEC-5879154D2B70 759 | 760 | 761 | workflowMetaData 762 | 763 | workflowTypeIdentifier 764 | com.apple.Automator.application 765 | 766 | 767 | 768 | -------------------------------------------------------------------------------- /man/cytofCore.extract.R.Rd: -------------------------------------------------------------------------------- 1 | \name{cytofCore.extract.R} 2 | \alias{cytofCore.extract.R} 3 | \alias{cytofCore.extract.native} 4 | \title{ 5 | Extraction of cells from CyToF IMD files 6 | } 7 | \description{ 8 | Identifies and extracts cells from CyToF IMD files using simple thresholding algorithm. Two implementations are availabe: in pure R, and with a C++ core. 9 | } 10 | \usage{ 11 | cytofCore.extract.R(imd, conf, pulse_thresh = 3, num_pushes = NULL, thresh = 10, sigma = 3, num_sigma = 3, min_length = 10, max_length = 75, noise.subtraction = TRUE, noise.min.length = 30, slope.filter = TRUE, freq = 77000) 12 | cytofCore.extract.native(imd, conf, pulse_thresh = 3, num_pushes = .Machine$integer.max, thresh = 10, sigma = 3, num_sigma = 3, min_length = 10, max_length = 75, noise.subtraction = TRUE, noise.min.length = 30, slope.filter = TRUE, freq = 77000) 13 | } 14 | \arguments{ 15 | \item{imd}{ 16 | IMD file 17 | } 18 | \item{conf}{ 19 | CyToF conf file or matrix. 20 | } 21 | \item{pulse_thresh}{ 22 | Pulse threshold used in dual count computation. 23 | } 24 | \item{num_pushes}{ 25 | Number of pushes to read. Default values reads to end of file. 26 | } 27 | \item{thresh}{ 28 | Threshold for start of a cell. 29 | } 30 | \item{sigma}{ 31 | Standard deviation of guassian filter applied to time series prior to thresholding. 32 | } 33 | \item{num_sigma}{ 34 | Number of sigma to extend gaussian filter. 35 | } 36 | \item{min_length}{ 37 | Minimum length of cell in pushes. 38 | } 39 | \item{max_length}{ 40 | Maximum length of cell in pushes. 41 | } 42 | \item{noise.subtraction}{ 43 | Subtract noise from cell counts. 44 | } 45 | \item{noise.min.length}{ 46 | Minimum length for valid noise region in pushes. 47 | } 48 | \item{slope.filter}{ 49 | Set cell quality to zero if slope has more than one zero crossing. 50 | } 51 | \item{freq}{ 52 | Number of pushes per second. 53 | } 54 | } 55 | \details{ 56 | Extracts cells from CyToF IMD file with conservative algorithm similar but not identical to that 57 | used by manufacturer's software. ".R" is a native R implementation, while ".native" is a C++-based 58 | implementation that is substantially more performant. 59 | } 60 | \value{ 61 | \item{cells.found }{Matrix of cells} 62 | \item{quality }{Quality metric, in [0,1] where 0 is lowest quality and 1 is highest quality} 63 | } 64 | \references{ 65 | Bandura, et al. Analytical Chemistry 81:6813-6822, 2009. 66 | } 67 | \author{ 68 | Michael Linderman (mlinderm@stanford.edu) 69 | } 70 | \examples{ 71 | } 72 | -------------------------------------------------------------------------------- /man/cytofCore.read.conf.Rd: -------------------------------------------------------------------------------- 1 | \name{cytofCore.read.conf} 2 | \alias{cytofCore.read.conf} 3 | \title{ 4 | Read CyToF produced conf file. 5 | } 6 | \description{ 7 | Read CyToF produced conf file. 8 | } 9 | \usage{ 10 | cytofCore.read.conf(file) 11 | } 12 | 13 | \arguments{ 14 | \item{file}{ 15 | Conf file. 16 | } 17 | } 18 | \details{ 19 | Expects CyToF-produced conf file with header line and entries with Symbol, 20 | Mass, R2, Intercept and Slope. 21 | } 22 | \value{ 23 | Matrix with the above described columns 24 | } 25 | \author{ 26 | Michael Linderman (mlinderm@stanford.edu) 27 | } 28 | \examples{ 29 | } 30 | -------------------------------------------------------------------------------- /man/cytofCore.read.imd.Rd: -------------------------------------------------------------------------------- 1 | \name{cytofCore.read.imd} 2 | \alias{cytofCore.read.imd} 3 | \title{ 4 | Read an CyToF IMD file 5 | } 6 | \description{ 7 | Read CyToF IMD binary file and return intensity/pulse data or dual count data 8 | } 9 | \usage{ 10 | cytofCore.read.imd(file, analytes = NULL, conf = NULL, pulse_thresh = 3, start_push = 0, num_pushes = NULL) 11 | } 12 | \arguments{ 13 | \item{file}{ 14 | IMD file 15 | } 16 | \item{analytes}{ 17 | Vector of analyte names. Length of vector must match number of analytes in IMD file. If NULL, \code{conf} must be provided. 18 | } 19 | \item{conf}{ 20 | CyToF conf file or matrix. If conf data is specified, only dual counts are returned. 21 | } 22 | \item{pulse_thresh}{ 23 | Pulse threshold used in dual count computation 24 | } 25 | \item{start_push}{ 26 | Starting push when reading from middle of file 27 | } 28 | \item{num_pushes}{ 29 | Number of pushes to read. NULL reads to end of file. 30 | } 31 | } 32 | \details{ 33 | Reads CyToF IMD binary file. 34 | 35 | IMD file contains intensity (I) and pulse data (P) for all analytes and pushes. Format of each push is 36 | 37 | I_analyte0 P_analyte0 I_analyte1 ... 38 | 39 | where all values are 16-bit unsigned integers. File starts with push 0. 40 | 41 | Dual counts are calculated as: 42 | 43 | dual = round(intensity * slope + intercept) 44 | if (dual < pulse_thresh) 45 | dual = max(dual, pulse) 46 | } 47 | \value{ 48 | \item{intensity }{Intensity data} 49 | \item{pulse }{Pulse data} 50 | \item{dual }{Dual counts} 51 | } 52 | \references{ 53 | Bandura, et al. Analytical Chemistry 81:6813-6822, 2009. 54 | } 55 | \author{ 56 | Michael Linderman (mlinderm@stanford.edu) 57 | } 58 | \note{ 59 | %% ~~further notes~~ 60 | } 61 | \examples{ 62 | } 63 | -------------------------------------------------------------------------------- /man/cytofCore.write.FCS.Rd: -------------------------------------------------------------------------------- 1 | \name{cytofCore.write.FCS} 2 | \alias{cytofCore.write.FCS} 3 | \title{ 4 | Write an FCS file 5 | } 6 | \description{ 7 | Write and FCS file from a data matrix. Specifically intended for use with cell data extracted from IMD files. 8 | } 9 | \usage{ 10 | cytofCore.write.FCS(x, filename, what = "numeric") 11 | } 12 | 13 | \arguments{ 14 | \item{x}{ 15 | A data matrix 16 | } 17 | \item{filename}{ 18 | A character scalar giving the output file name 19 | } 20 | \item{what}{ 21 | A character scale defining the output data type. One in 'integer', 'numeric', 'double'. Note that forcing the data type to 'integer' may result in considerable loss of precision. We recommend using the default data type. 22 | } 23 | } 24 | \details{ 25 | Create FCS 3.0 standard file from the input data matrix. 26 | } 27 | \value{ 28 | A character scale of the file name. 29 | } 30 | \references{ 31 | \url{http://www.isac-net.org} 32 | } 33 | \author{ 34 | Michael Linderman (mlinderm@stanford.edu) 35 | } 36 | \seealso{ 37 | \code{\link{write.FCS}} 38 | } 39 | \examples{ 40 | } 41 | --------------------------------------------------------------------------------