PlotHVGVariance

Plot variance for all genes (features) on a geneda object using ggplot2.

Usage

PlotHVGVariance(object, transform = NULL, dropTopN = 0)

Arguments

object

A geneda object created by GenEDA().

transform

One of c("log") to log-transform variance, or NULL for none. Default = NULL

dropTopN

Number of top-most variable genes to drop prior to plotting. Default = 0

Value

A ggplot2 object visualizing the variance of HVGs

Examples

data(Snail1KO)
counts <- as.matrix(Snail1KO$rawCounts)
counts <- counts[rowSums(counts >= 10) >= 3, ]
meta <- Snail1KO$metadata
rownames(meta) <- meta$Sample
norm <- log2(t(t(counts) / colSums(counts)) * 1e6 + 1)
obj <- GenEDA(normalized = norm, metadata = meta, counts = counts)
PlotHVGVariance(obj, transform = "log")