compareSCEs: Compare SingleCellExperiment objects

Description Usage Arguments Details Value Examples

View source: R/compare.R

Description

Combine the data from several SingleCellExperiment objects and produce some basic plots comparing them.

Usage

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compareSCEs(sces, point.size = 0.1, point.alpha = 0.1, fits = TRUE,
  colours = NULL)

Arguments

sces

named list of SingleCellExperiment objects to combine and compare.

point.size

size of points in scatter plots.

point.alpha

opacity of points in scatter plots.

fits

whether to include fits in scatter plots.

colours

vector of colours to use for each dataset.

Details

The returned list has three items:

FeatureData

Combined feature data from the provided SingleCellExperiments.

PhenoData

Combined pheno data from the provided SingleCellExperiments.

Plots

Comparison plots

Means

Boxplot of mean distribution.

Variances

Boxplot of variance distribution.

MeanVar

Scatter plot with fitted lines showing the mean-variance relationship.

LibraySizes

Boxplot of the library size distribution.

ZerosGene

Boxplot of the percentage of each gene that is zero.

ZerosCell

Boxplot of the percentage of each cell that is zero.

MeanZeros

Scatter plot with fitted lines showing the mean-zeros relationship.

The plots returned by this function are created using ggplot and are only a sample of the kind of plots you might like to consider. The data used to create these plots is also returned and should be in the correct format to allow you to create further plots using ggplot.

Value

List containing the combined datasets and plots.

Examples

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sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
comparison <- compareSCEs(list(Splat = sim1, Simple = sim2))
names(comparison)
names(comparison$Plots)

splatter documentation built on Dec. 7, 2018, 6 p.m.