visGene: Visualize gene expression pattern in scRNA-seq

In zhijinwu/SC2P: Two phase differential expression for singel-cell RNA-seq

Usage

visGene(names, sc2p.obj, group.name = NULL, low.prob = 0.99, show.name = TRUE, show.points = T, all.points = T, annotation = NULL)

Arguments

names	Character for the name of a gene.
sc2p.obj	An object of sc2pSet, result from the eset2Phase function.
group.name	Character for the name of factors indicating the experimental conditions. This has to be the name of a column in pData(sc2p.obj) data frame.
low.prob	?????????????
show.name	Logical to indicate whether to show the name of genes as the tileof the figure.
show.points	???????????????????
all.points	???????????????????
annotation	???????????????????

Author(s)

Zhijin (Jean) Wu <[e-mail]>

See Also

eset2Phase, twoPhaseDE, topGene

Examples

## Not run: 
data(brain_scRNAseq)

## create ExpressionSet
colnames(Y) <- rownames(design)
phenoData <- new("AnnotatedDataFrame", data=design)
eset <- ExpressionSet(assayData=Y, phenoData=phenoData)

## infer latent status
data <- eset2Phase(eset)

## test DE
de.sc2p <- twoPhaseDE(data, design="celltype", test.which=1, offset="sf")

## visualize top phase I DE gene
visGene(topGene(de.sc2p, 1)$Gene.name[1], data, group.name="celltype")

## visualize top phase II DE gene
visGene(topGene(de.sc2p, 2)$Gene.name[1], data, group.name="celltype")

## End(Not run)

zhijinwu/SC2P documentation built on May 16, 2019, 9:13 p.m.