character, numeric or logical vector indicating a set of
features to plot. If character, entries must all be in
featureNames(object). If numeric, values are taken to be indices for
features. If logical, vector is used to index features and should have length
equal to nrow(object). If NULL, then the function checks if
feature controls are defined. If so, then only feature controls are plotted,
if not, then all features are plotted.
feature_controls
character, numeric or logical vector indicating a set of
features to be used as feature controls for computing technical dropout
effects. If character, entries must all be in featureNames(object). If
numeric, values are taken to be indices for features. If logical, vector is
used to index features and should have length equal to nrow(object).
If NULL, then the function checks if feature controls are defined. If
so, then these feature controls are used.
shape
(optional) numeric scalar to define the plotting shape.
alpha
(optional) numeric scalar (in the interval 0 to 1) to define the
alpha level (transparency) of plotted points.
...
further arguments passed to plotMetadata (should
only be size, if anythin).
Details
This function plots gene expression frequency versus mean
expression level, which can be useful to assess the effects of technical
dropout in the dataset. We fit a non-linear least squares curve for the
relationship between expression frequency and mean expression and use this to
define the number of genes above high technical dropout and the numbers of
genes that are expressed in at least 50
of genes to be treated as feature controls can be specified, otherwise any
feature controls previously defined are used.
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/plotExprsFreqVsMean.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotExprsFreqVsMean
> ### Title: Plot frequency of expression against mean expression level
> ### Aliases: plotExprsFreqVsMean
>
> ### ** Examples
>
> data("sc_example_counts")
> data("sc_example_cell_info")
> pd <- new("AnnotatedDataFrame", data=sc_example_cell_info)
> rownames(pd) <- pd$Cell
> ex_sceset <- newSCESet(countData=sc_example_counts, phenoData=pd)
> ex_sceset <- calculateQCMetrics(ex_sceset)
> plotExprsFreqVsMean(ex_sceset)
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.