plot-methods | R Documentation |
Identified doppelgangers are shown with a red vertical line overlaid on a histogram of pairwise sample correlations. One plot is made per pair of datasets.
## S4 method for signature 'DoppelGang,ANY'
plot(x, skip.no.doppels = FALSE, plot.pair = NULL, ...)
x |
An object of class |
skip.no.doppels |
(default FALSE) If TRUE, do not plot histograms where no doppelgangers were identified. |
plot.pair |
An optional character vector of length two, providing the names of two datasets. If provided, only the comparison of these two datasets will be plotted. |
... |
Additional arguments passed on to |
None
Histograms of all pairwise sample correlations, showing identified doppelgangers.
Levi Waldron
library(curatedOvarianData)
data(TCGA_eset)
data(GSE26712_eset)
## Remove some TCGA samples to speed computation:
keep.tcga <-
c("TCGA.13.2060", "TCGA.24.2290", "TCGA.25.2392", "TCGA.25.2404",
"TCGA.59.2349", "TCGA.09.2044", "TCGA.24.2262", "TCGA.24.2293",
"TCGA.25.2393", "TCGA.25.2408", "TCGA.59.2350", "TCGA.09.2045",
"TCGA.24.2267", "TCGA.59.2351", "TCGA.09.2048", "TCGA.24.2271",
"TCGA.24.2298", "TCGA.25.2398", "TCGA.59.2354", "TCGA.09.2050",
"TCGA.24.2281", "TCGA.09.2051", "TCGA.29.2428", "TCGA.09.2055",
"TCGA.24.2289", "TCGA.29.2414", "TCGA.59.2352", "TCGA.36.2532",
"TCGA.36.2529", "TCGA.36.2551", "TCGA.42.2590", "TCGA.13.2071",
"TCGA.29.2432", "TCGA.36.2537", "TCGA.36.2547", "TCGA.04.1369",
"TCGA.42.2591", "TCGA.23.2641", "TCGA.29.2434", "TCGA.36.2538",
"TCGA.36.2548", "TCGA.04.1516", "TCGA.42.2593", "TCGA.36.2549",
"TCGA.04.1644", "TCGA.13.2057", "TCGA.23.2647", "TCGA.36.2530",
"TCGA.36.2552", "TCGA.42.2587", "TCGA.13.2061", "TCGA.42.2588",
"TCGA.36.2544", "TCGA.42.2589", "TCGA.13.2066", "TCGA.61.2613",
"TCGA.61.2614", "TCGA.24.1852", "TCGA.29.1704", "TCGA.13.1819"
)
keep.tcga <- unique(c(keep.tcga, sampleNames(TCGA_eset)[1:200]))
testesets <- list(Bonome08=GSE26712_eset, TCGA=TCGA_eset[, keep.tcga])
results1 <- doppelgangR(testesets,
corFinder.args=list(use.ComBat=FALSE), phenoFinder.args=NULL,
cache.dir=NULL)
plot(results1)
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