Compare SingleCellExperiment objects

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

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.

Value

List containing the combined datasets and plots.

Details

The returned list has three items:

RowData

Combined row data from the provided SingleCellExperiments.

ColData

Combined column 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.

LibrarySizes

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.

VarGeneCor

Heatmap of correlation of the 100 most variable genes.

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.

Examples

sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
#> Getting parameters...
#> Creating simulation object...
#> Simulating library sizes...
#> Simulating gene means...
#> Simulating BCV...
#> Simulating counts...
#> Simulating dropout (if needed)...
#> Done!
sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
#> Simulating means...
#> Simulating counts...
#> Creating final dataset...
comparison <- compareSCEs(list(Splat = sim1, Simple = sim2))
names(comparison)
#> [1] "RowData" "ColData" "Plots"  
names(comparison$Plots)
#> [1] "Means"        "Variances"    "MeanVar"      "LibrarySizes" "ZerosGene"   
#> [6] "ZerosCell"    "MeanZeros"    "VarGeneCor"