an SCESet object containing expression values and
experimental information. Must have been appropriately prepared.
aesth
aesthetics function call to pass to ggplot. This function
expects at least x and y variables to be supplied. The default is to produce
a density plot of number of cells expressing the feature (requires
calculateQCMetrics to have been run on the SCESet object prior).
theme_size
numeric scalar giving default font size for plotting theme
(default is 10).
...
arguments passed to plotMetadata.
Details
Plot feature (gene) data 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/plotFeatureData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotFeatureData
> ### Title: Plot feature (gene) data from an SCESet object
> ### Aliases: plotFeatureData
>
> ### ** 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)
> plotFeatureData(example_sceset, aesth=aes(x=n_cells_exprs, y=pct_total_counts))
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.