flowStats quadrantGate and 'names'
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Aric Gregson ▴ 270
@aric-gregson-3058
Last seen 7.2 years ago
Hello, I have used the 'names' function in flowViz to place percents of the gated population within the plot. I have never figured out how to get the stats placed in the plot automatically, but at least I could place the numbers in the plot. With quadrantGate plots the 'names' function does not appear to do anything. Is there a mechanism to access this and label the plot quadrants? Thanks, Aric
flowViz flowViz • 666 views
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@nishant-gopalakrishnan-3253
Last seen 7.2 years ago
Hi Aric, I am not sure what 'names' function in flowViz you are talking about. I do not see one in flowViz. Its hard to guess what you have done without providing some reproducible lines of code. With regard to putting in custom labels inside the plots. (if that?s what you are trying to do) FlowViz does not have a direct option of placing the the summary stats/custom text inside the plots. However, if you are keen of placing some of the labels/summary stats that you need on the plot, it can be done but will require some extra effort. 1. You will need to create a custom panel function that does what you need and pass this to the panel argument of the xyplot function in flowViz. 2. Please have a look at the panel.xyplot.flowFrame method in the flowViz package You will need to modify this to add your text label. You could add something like gltext(xposition, yposition, "your label",..., gp= gpar$gate.text) after the polygon is drawn to add a label at the position (xposition, yposition) on the plot. 3. Call xyplot with the panel argument set to the function that you just modified Nishant On 09/23/2010 12:54 PM, Aric Gregson wrote: > Hello, > > I have used the 'names' function in flowViz to place percents of the > gated population within the plot. I have never figured out how to get > the stats placed in the plot automatically, but at least I could place > the numbers in the plot. With quadrantGate plots the 'names' function > does not appear to do anything. Is there a mechanism to access this and > label the plot quadrants? > > Thanks, Aric > > _______________________________________________ > 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 >
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On Thu, 23 Sep 2010 14:48:38 -0700 Nishant Gopalakrishnan <ngopalak at="" fhcrc.org=""> wrote: > I am not sure what 'names' function in flowViz you are talking about. > I do not see one in flowViz. Its hard to guess what you have done > without providing some reproducible lines of code. > > With regard to putting in custom labels inside the plots. (if that?s > what you are trying to do) FlowViz does not have a direct option of > placing the the summary stats/custom text inside the plots. I see that it appears to have been removed from flowViz. Previously, if set 'names=TRUE', the name of the gated population (i.e., filterName) would be printed on the plot near the gate outline. I had modified it as below to include percentages of parent populations. Most flow software does this automatically as an option. Here is an example that I have used in published figures: plot344livebw <-xyplot(`Indo.1..Violet..A` ~ `APC.H7.A`, Data(wf[["logicle"]])[[6]], ylim=c(-1,11.75), smooth=F, alpha=0.5, col="grey70", scales=list(tick.number=6), aspect="iso", filter=livefilter, names="\n6.3%", main="Live CD4 Gate\nSinglet+", xlab = "CD4 APC-H7", ylab = "UV Blue Live/Dead", par.settings=list(gate=list(col="grey10", alpha=.5), gate.text=list(col="black", alpha=0.3, cex=2))) So, it used to do something. > However, if you are keen of placing some of the labels/summary stats > that you need on the plot, it can be done but will require some extra > effort. > > 1. You will need to create a custom panel function that does what you > need and pass this to the panel argument of the xyplot function in > flowViz. 2. Please have a look at the panel.xyplot.flowFrame method > in the flowViz package You will need to modify this to add your text > label. You could add something like > gltext(xposition, yposition, "your label",..., gp= gpar$gate.text) > after the polygon is drawn to add a label at the position (xposition, > yposition) on the plot. > 3. Call xyplot with the panel argument set to the function that you > just modified I will give this a try... Thanks, Aric
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