flowcore/flowviz filter
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Guest User ★ 12k
@guest-user-4897
Last seen 7.3 years ago
Hi! I am using flowCore and flowViz for interpreting flow cytometry data. I need a filter for the graphics in which I only choose the regions that have high density points in a plot, for example, of the columns FL1.log vs FS.Log, and I know there is one, but I don't find it. I will thank your help. -- output of sessionInfo(): R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
flowCore flowViz flowCore flowViz • 977 views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 8 weeks ago
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You might be thinking of |cur2Filter|. Here is an example |library(flowViz) data(GvHD) fr <- GvHD[[2]] #transform the data trs <- logTransform() fr_trans <- transform(fr,`FL1-H` = trs(`FL1-H`),`FL2-H` = trs(`FL2-H`)) #use flowCore::curv2Filter cf <- curv2Filter(x="FL1-H", y ="FL2-H", filterId ="s5a02", bwFac =4.5) #fres <- filter() xyplot(`FL1-H`~`FL2-H`, fr_trans, smooth =F, xbin =64, filter = cf) | Alternatively, you can use |flowClust.2d| from |openCyto| package to gate out the target population more precisely. |library(openCyto) # use openCyto::flowclust fres <- flowClust.2d(fr = fr_trans, xChannel ="FL1-H", yChannel ="FL2-H", K=2, target = c(3,2)) xyplot(`FL1-H`~`FL2-H`, fr_trans, smooth =F, xbin =64, filter = fres) | Also, you want to check out http://opencyto.org/ for a more *robust framework of automated flow data analysis* . Mike Jiang On 02/19/2014 08:32 AM, Nacho [guest] wrote: > Hi! > > I am using flowCore and flowViz for interpreting flow cytometry data. I need a filter for the graphics in which I only choose the regions that have high density points in a plot, for example, of the columns FL1.log vs FS.Log, and I know there is one, but I don't find it. > > I will thank your help. > > > -- output of sessionInfo(): > > R version 2.14.1 (2011-12-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C > [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 > [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org.
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