plot a gating tree

Description

Plot a tree/graph representing the GatingHierarchy

Usage

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## S4 method for signature 'GatingSet,missing'
plot(x, y, ...)

## S4 method for signature 'GatingSet,character'
plot(x, y, ...)

Arguments

x

GatingHierarchy or GatingSet. If GatingSet, the first sample will be used to extract gating tree.

y

missing or character specifies.

...

other arguments:

  • boolean: TRUE|FALSE logical specifying whether to plot boolean gate nodes. Defaults to FALSE.

  • showHidden: TRUE|FALSE logical whether to show hidden nodes

  • dir: character Default is NULL, which render the gating tree in regular R plot device. Otherwise it specifies a folder where the gating tree is output to a svg image with some interactivity (e.g. when click on each node, the actual gates will be displayed) This interactivity currently only works when the svg is rendered within a HTML webpage (e.g. generated as knitr report)

  • svg.par: a list of parameters passed to devSVGTips

  • png.par: a list of parameters passed to png

  • layout: See layoutGraph in package Rgraphviz

  • width: See layoutGraph in package Rgraphviz

  • height: See layoutGraph in package Rgraphviz

  • fontsize: See layoutGraph in package Rgraphviz

  • labelfontsize: See layoutGraph in package Rgraphviz

  • fixedsize: See layoutGraph in package Rgraphviz

Examples

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## Not run: 
 #gs is a GatingSet
 plot(gs) # the same as plot(gs[[1]])
 #plot a substree rooted from 'CD4'
 plot(gs, "CD4")

 # output as svg format with onclick event of each node displaying the gate(saved as png files) within pop-up window
 plot(gs[[1]], dir = "myFolder")

 # customize the size of svg and png files
 plot(gh, dir = "myFolder", svg.par =list(width = 7, height = 7), png.par = list(width = 200, height = 200)

 #each node link to multiple gates across samples
 #here is the example code showing how to embed
 #the svg output within knitr quick report

 #+ eval=T, results = "asis", message = F
 svgFile <- plot(gs, dir = './svg', svg.par =list(width = 7, height = 7), png.par = list(width = 400, height = 400 ))
 cat("<embed src=", svgFile, " type='image/svg+xml' />", sep = "")

## End(Not run)

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