a data.frame (or object that can be coerced to such) object
containing metadata in columns to plot.
aesth
aesthetics function call to pass to ggplot. This function
expects at least x and y variables to be supplied. The default is to plot
total_features against log10(total_counts).
shape
numeric scalar to define the plotting shape. Ignored if shape is
included in the aesth argument.
alpha
numeric scalar (in the interval 0 to 1) to define the alpha
level (transparency) of plotted points. Ignored if alpha is included in the
aesth argument.
size
numeric scalar to define the plotting size. Ignored if size is
included in the aesth argument.
theme_size
numeric scalar giving default font size for plotting theme
(default is 10)
Details
Plot cell or feature metadata from an SCESet object. If one variable
is supplied then a density plot will be returned. If both variables are
continuous (numeric) then a scatter plot will be returned. If one variable is
discrete and one continuous then a violin plot with jittered points overlaid
will be returned. If both variables are discrete then a jitter plot will be
produced. The object returned is a ggplot object, so further layers and
plotting options (titles, facets, themes etc) can be added.
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/plotMetadata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMetadata
> ### Title: Plot metadata for cells or features
> ### Aliases: plotMetadata
>
> ### ** 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)
> example_sceset <- calculateQCMetrics(example_sceset)
> plotMetadata(pData(example_sceset))
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.