if TRUE, a density scatter plot is plotted. This plot shows the density of the data.
sample
An integer, indicating the number of subsamples to take for the density scatterplot. This is only recommended if the data is very large, as the density computation takes some time.
cluster
if cluster=T, the experiments are clustered and similiar experiments are plotted together.
##
points <- 10^4
x <- rnorm(points/2)
x <- c(x,x+2.5)
x <- sign(x)*abs(x)^1.3
y <- x + rnorm(points,sd=0.8)
mat <- matrix(c(x,y), ncol=2)
colnames(mat) <- c("a", "b")
plotScatter(mat, density=TRUE)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(Starr)
Loading required package: Ringo
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: RColorBrewer
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
Loading required package: affy
Attaching package: 'affy'
The following object is masked from 'package:Ringo':
probes
Loading required package: affxparser
Attaching package: 'Starr'
The following object is masked from 'package:affy':
plotDensity
The following object is masked from 'package:limma':
plotMA
The following object is masked from 'package:BiocGenerics':
plotMA
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Starr/plot.scatter.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotScatter
> ### Title: High level scatterplot of experiments
> ### Aliases: plotScatter
> ### Keywords: hplot
>
> ### ** Examples
>
> ##
> points <- 10^4
> x <- rnorm(points/2)
> x <- c(x,x+2.5)
> x <- sign(x)*abs(x)^1.3
> y <- x + rnorm(points,sd=0.8)
> mat <- matrix(c(x,y), ncol=2)
> colnames(mat) <- c("a", "b")
> plotScatter(mat, density=TRUE)
>
>
>
>
>
> dev.off()
null device
1
>