plotNhoodCounts: Plot the number of cells in a neighbourhood per sample and...

In MikeDMorgan/miloR: Differential neighbourhood abundance testing on a graph

Plot the number of cells in a neighbourhood per sample and condition

Description

Plot the number of cells in a neighbourhood per sample and condition

Usage

plotNhoodCounts(x, subset.nhoods, design.df, condition, n_col = 3)

Arguments

x	A Milo object with a non-empty nhoodCounts slot.
subset.nhoods	A logical, integer or character vector indicating the rows of nhoodCounts(x) to use for plotting. If you use a logical vector, make sure the length matches nrow(nhoodCounts(x)).
design.df	A data.frame which matches samples to a condition of interest. The row names should correspond to the samples. You can use the same design.df that you already used in the testNhoods function.
condition	String specifying the condition of interest Has to be a column in the design.
n_col	Number of columns in the output ggplot.

Value

A ggplot-class object

Author(s)

Nick Hirschmüller

Examples

require(SingleCellExperiment)
ux.1 <- matrix(rpois(12000, 5), ncol=300)
ux.2 <- matrix(rpois(12000, 4), ncol=300)
ux <- rbind(ux.1, ux.2)
vx <- log2(ux + 1)
pca <- prcomp(t(vx))

sce <- SingleCellExperiment(assays=list(counts=ux, logcounts=vx),
                            reducedDims=SimpleList(PCA=pca$x))
milo <- Milo(sce)
milo <- buildGraph(milo, k=20, d=10, transposed=TRUE)
milo <- makeNhoods(milo, k=20, d=10, prop=0.3)
milo <- calcNhoodDistance(milo, d=10)

cond <- sample(c("A","B","C"),300,replace=TRUE)

meta.df <- data.frame(Condition=cond, Replicate=c(rep("R1", 100), rep("R2", 100), rep("R3", 100)))
meta.df$SampID <- paste(meta.df$Condition, meta.df$Replicate, sep="_")
milo <- countCells(milo, meta.data=meta.df, samples="SampID")

design.mtx <- data.frame("Condition"=c(rep("A", 3), rep("B", 3), rep("C",3)),
                         "Replicate"=rep(c("R1", "R2", "R3"), 3))
design.mtx$SampID <- paste(design.mtx$Condition, design.mtx$Replicate, sep="_")
rownames(design.mtx) <- design.mtx$SampID

plotNhoodCounts(x = milo,
                subset.nhoods = c(1,2),
                design.df = design.mtx,
                condition = "Condition")

MikeDMorgan/miloR documentation built on Feb. 29, 2024, 6:20 p.m.