openCyto displaying gating panels
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Entering edit mode
Rivka • 0
@rivka-11959
Last seen 4.3 years ago
Munich

Hello,

when displaying my gating panels with plotGate(gh), I get all panels in one window, as I like it.

I now need to customize the axises for some of the panels separately but cannot find a function to still have all panels showing in one window in a 4*4 arrangement. The following shows them in 3 separated windows.

plotGate(gh,c("Lymphocytes"), xlim =  c(-2e6, 1e7) , ylim = c(995e0, 1001e0))
plotGate(gh,c("Single Cells"),xlim = c(5e4, 4e5), ylim = c(1e2, 25e1) )
plotGate(gh,c("CD3"), xlim = c(5e4, 4e5), ylim = c(0,3e2) )

I would like these 3 and another four gates A, B, C, D in one window.

Can anybody please give me an idea?

Thanks, Rivka

opencyto • 629 views
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Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 23 days ago

"plotGate " method for "GatingHierarchy" object (i.e. 'gh' in your case) is implemented by using "gridExtra::grid.arrange" to put multiple plots on the same page. If you need to customize each individual panel/plot to that extent, you disable default arrange behavior for "plotGate' call so that it will return a "trellis plot" object that can be arranged later on your own. e.g.

p1 <- plotGate(gh,c("Lymphocytes"), xlim =  c(-2e6, 1e7) , ylim = c(995e0, 1001e0), arrange = FALSE)

p2 <- plotGate(gh,c("Single Cells"),xlim = c(5e4, 4e5), ylim = c(1e2, 25e1), arrange = FALSE)
p3 <- plotGate(gh,c("CD3"), xlim = c(5e4, 4e5), ylim = c(0,3e2), arrange = FALSE)

....#the same as your A, B, C, D plots

plotObjs <- c(p1, p2, p3, A, B, C, D)

gridExtra::grid.arrange(grobs = plotObjs, nrow = 4, ncol = 4)