an SCESet object with a non-NULL reducedDimension
slot.
...
optional arguments (from those listed above) passed to
plotReducedDim.SCESet or plotReducedDim.default
df_to_plot
data.frame containing a reduced dimension represenation of
cells and optional metadata for the plot.
ncomponents
numeric scalar indicating the number of principal
components to plot, starting from the first principal component. Default is
2. If ncomponents is 2, then a scatterplot of Dimension 2 vs Dimension
1 is produced. If ncomponents is greater than 2, a pairs plots for the
top dimensions is produced.
colour_by
character string defining the column of pData(object) to
be used as a factor by which to colour the points in the plot.
shape_by
character string defining the column of pData(object) to
be used as a factor by which to define the shape of the points in the plot.
size_by
character string defining the column of pData(object) to
be used as a factor by which to define the size of points in the plot.
percentVar
numeric vector giving the proportion of variance in
expression explained by each reduced dimension. Only expected to be used
internally in the plotPCA function.
theme_size
numeric scalar giving default font size for plotting theme
(default is 10).
legend
character, specifying how the legend(s) be shown? Default is
"auto", which hides legends that have only one level and shows others.
Alternatives are "all" (show all legends) or "none" (hide all legends).
Details
The function plotReducedDim.default assumes that the first
ncomponents columns of df_to_plot contain the reduced dimension
components to plot, and that any subsequent columns define factors for
colour_by, shape_by and size_by in the plot.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
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(scater)
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: ggplot2
Attaching package: 'scater'
The following object is masked from 'package:stats':
filter
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/scater/plotReducedDim.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotReducedDim
> ### Title: Plot reduced dimension representation of cells
> ### Aliases: plotReducedDIm plotReducedDim plotReducedDim,SCESet-method
> ### plotReducedDim,data.frame-method plotReducedDim.SCESet
> ### plotReducedDim.default
>
> ### ** Examples
>
> data("sc_example_counts")
> data("sc_example_cell_info")
> pd <- new("AnnotatedDataFrame", data = sc_example_cell_info)
> example_sceset <- newSCESet(countData = sc_example_counts, phenoData = pd)
> drop_genes <- apply(exprs(example_sceset), 1, function(x) {var(x) == 0})
> example_sceset <- example_sceset[!drop_genes, ]
>
> reducedDimension(example_sceset) <- prcomp(t(exprs(example_sceset)), scale. = TRUE)$x
> plotReducedDim(example_sceset)
> plotReducedDim(example_sceset, colour_by="Cell_Cycle")
> plotReducedDim(example_sceset, colour_by="Cell_Cycle", shape_by="Treatment")
> plotReducedDim(example_sceset, colour_by="Cell_Cycle", size_by="Treatment")
Warning message:
Using size for a discrete variable is not advised.
> plotReducedDim(example_sceset, ncomponents=5)
> plotReducedDim(example_sceset, ncomponents=5, colour_by="Cell_Cycle", shape_by="Treatment")
>
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
