basicplot functionality (flowCore/rflowcyt)
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M. Jankowski ▴ 160
@m-jankowski-2199
Last seen 10.3 years ago
Hi All, Thank you for helping me out with all my questions. I am new to R and really appreciate your guidance. Here is my new question: In this document: www.ficcs.org/meetings/ficcs2/presentations/NolwennLeMeur-Nov2006.pdf - there is this excellent figure showing just how the data has been gated out. The figure appears to be plotted by basicplot: basicplot(data,gateddata) There are several examples with different geometries. Based on the notes in the presentation, it looks like this function is in the flowcore library. How do I achieve this very useful effect? Thanks! Matt
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Byron Ellis ▴ 100
@byron-ellis-2138
Last seen 10.3 years ago
That document is somewhat out of date. For simple plotting (i.e. not drawing a selected region of any sort), plot(<frame>,<optional vector="" of="" 1="" or="" 2="" parameters="">) will give you the smooth scatter plot when two parameters are given (it defaults to FCS and SSC) and a histogram if only one is given. For more general plotting, including being able to draw a filter onto a plot among other things, you'll mostly want the flowViz package. IIRC the function called "basicplot" is now in that package and known as "flowPlot." Additionally, many of the lattice plotting methods have been adapted for use with flow data and do sensible things, including drawing a filter onto a plot. On 8/11/07, M. Jankowski <mjankowski at="" gmail.com=""> wrote: > Hi All, > > Thank you for helping me out with all my questions. I am new to R and > really appreciate your guidance. Here is my new question: > > In this document: > > www.ficcs.org/meetings/ficcs2/presentations/NolwennLeMeur- Nov2006.pdf - > > there is this excellent figure showing just how the data has been > gated out. The figure appears to be plotted by basicplot: > basicplot(data,gateddata) > > There are several examples with different geometries. Based on the > notes in the presentation, it looks like this function is in the > flowcore library. How do I achieve this very useful effect? > > Thanks! > Matt > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Byron Ellis (byron.ellis at gmail.com) "Oook" -- The Librarian
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> For more general plotting, including being able to draw a filter onto > a plot among other things, you'll mostly want the flowViz package. > IIRC the function called "basicplot" is now in that package and known > as "flowPlot." Additionally, many of the lattice plotting methods have > been adapted for use with flow data and do sensible things, including > drawing a filter onto a plot. > Byron, Thank you for helping to me find the right direction on this. Is there a HowTo for flowViz that I might follow? I tried help(flowPlot) but the resulting documentaton seemed incomplete. I'd like to do things like draw a filter and/or see a filter I set from the command line on the plot. Thanks! Matt
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On 8/12/07, M. Jankowski <mjankowski at="" gmail.com=""> wrote: > > For more general plotting, including being able to draw a filter onto > > a plot among other things, you'll mostly want the flowViz package. > > IIRC the function called "basicplot" is now in that package and known > > as "flowPlot." Additionally, many of the lattice plotting methods have > > been adapted for use with flow data and do sensible things, including > > drawing a filter onto a plot. > > > Byron, > > Thank you for helping to me find the right direction on this. > > Is there a HowTo for flowViz that I might follow? I tried > help(flowPlot) but the resulting documentaton seemed incomplete. I'd > like to do things like draw a filter and/or see a filter I set from > the command line on the plot. The support for filters in flowViz was added after the current bioc release. If you go to the page for the devel version, you'll find a link to a (somewhat terse) vignette with examples: http://bioconductor.org/packages/2.1/bioc/html/flowViz.html To use this (the filter stuff), you either need to run R-devel, or manually install flowViz for R 2.5.x (I don't think there will be any problems if you do that, but I can't guarantee it). -Deepayan
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> The support for filters in flowViz was added after the current bioc > release. If you go to the page for the devel version, you'll find a > link to a (somewhat terse) vignette with examples: > > http://bioconductor.org/packages/2.1/bioc/html/flowViz.html > > To use this (the filter stuff), you either need to run R-devel, or > manually install flowViz for R 2.5.x (I don't think there will be any > problems if you do that, but I can't guarantee it). > > -Deepayan Deepayan, Thank you for your answer to my question. I feel like I am getting on the right track to visualize flow data. When I attempted to install flowViz 1.1.4: > install.packages("flowViz_1.1.4.tar.gz", repos=NULL) I receive this error (the whole sequence is below): > Error in importIntoEnv(impenv, impnames, ns, impvars) : object 'ecdfplot' is not exported by 'namespace:latticeExtra' Do I need to install the dev version of lattice or just go ahead and install R-dev? I'm guessing that ecdfplot is not in the current widely available version of lattice. I appreciate any advice you might have for me. Thanks! Matt > install.packages("flowViz_1.1.4.tar.gz", repos=NULL) Warning in install.packages("flowViz_1.1.4.tar.gz", repos = NULL) : argument 'lib' is missing: using '/home/mdj/R/i486-pc-linux- gnu-library /2.5' * Installing *source* package 'flowViz' ... ** R ** inst ** preparing package for lazy loading Loading required package: flowCore Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: rrcov Scalable Robust Estimators with High Breakdown Point (version 0.3-06) KernSmooth 2.22 installed Copyright M. P. Wand 1997 Loading required package: rgl Loading required package: geneplotter Loading required package: annotate Loading required package: lattice Loading required package: MASS Error in importIntoEnv(impenv, impnames, ns, impvars) : object 'ecdfplot' is not exported by 'namespace:latticeExtra' Execution halted ERROR: lazy loading failed for package 'flowViz' ** Removing '/home/mdj/R/i486-pc-linux-gnu-library/2.5/flowViz' ** Restoring previous '/home/mdj/R/i486-pc-linux-gnu- library/2.5/flowViz' Warning message: installation of package 'flowViz_1.1.4.tar.gz' had non-zero exit status in: inst all.packages("flowViz_1.1.4.tar.gz", repos = NULL) >
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On 8/12/07, M. Jankowski <mjankowski at="" gmail.com=""> wrote: > > The support for filters in flowViz was added after the current bioc > > release. If you go to the page for the devel version, you'll find a > > link to a (somewhat terse) vignette with examples: > > > > http://bioconductor.org/packages/2.1/bioc/html/flowViz.html > > > > To use this (the filter stuff), you either need to run R-devel, or > > manually install flowViz for R 2.5.x (I don't think there will be any > > problems if you do that, but I can't guarantee it). > > > > -Deepayan > > Deepayan, > > Thank you for your answer to my question. I feel like I am getting on > the right track to visualize flow data. When I attempted to install > flowViz 1.1.4: > > > install.packages("flowViz_1.1.4.tar.gz", repos=NULL) > > I receive this error (the whole sequence is below): > > > Error in importIntoEnv(impenv, impnames, ns, impvars) : > object 'ecdfplot' is not exported by 'namespace:latticeExtra' > > Do I need to install the dev version of lattice or just go ahead and > install R-dev? I'm guessing that ecdfplot is not in the current widely > available version of lattice. I appreciate any advice you might have > for me. The dependency is actually a different package called 'latticeExtra'. Just get the latest version from CRAN. -Deepayan > Thanks! > Matt > > > install.packages("flowViz_1.1.4.tar.gz", repos=NULL) > Warning in install.packages("flowViz_1.1.4.tar.gz", repos = NULL) : > argument 'lib' is missing: using '/home/mdj/R/i486-pc- linux-gnu-library > /2.5' > * Installing *source* package 'flowViz' ... > ** R > ** inst > ** preparing package for lazy loading > Loading required package: flowCore > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: rrcov > Scalable Robust Estimators with High Breakdown Point (version 0.3-06) > KernSmooth 2.22 installed > Copyright M. P. Wand 1997 > Loading required package: rgl > Loading required package: geneplotter > Loading required package: annotate > Loading required package: lattice > Loading required package: MASS > Error in importIntoEnv(impenv, impnames, ns, impvars) : > object 'ecdfplot' is not exported by 'namespace:latticeExtra' > Execution halted > ERROR: lazy loading failed for package 'flowViz' > ** Removing '/home/mdj/R/i486-pc-linux-gnu-library/2.5/flowViz' > ** Restoring previous '/home/mdj/R/i486-pc-linux-gnu- library/2.5/flowViz' > Warning message: > installation of package 'flowViz_1.1.4.tar.gz' had non-zero exit status in: inst > all.packages("flowViz_1.1.4.tar.gz", repos = NULL) > > >
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Deepayan, Thank you! Matt
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