plot-SegmentedCellExperiment: A basic plot for SegmentedCellExperiment object

In ellispatrick/SegmentedCellExperiment: S4 Class for segmented spatial 'omics data

Description

This function generates a basic plot of the location and cellType data.

Arguments

x	A SegmentedCellExperiment object.
imageID	The image that should be plotted.

Value

A ggplot object.

usage

'plot(x, imageID = NULL)'

Examples

### Something that resembles cellProfiler data

set.seed(51773)

n = 10

cells <- data.frame(row.names = seq_len(n))
cells$ObjectNumber <- seq_len(n)
cells$ImageNumber <- rep(1:2,c(n/2,n/2))
cells$AreaShape_Center_X <- runif(n)
cells$AreaShape_Center_Y <- runif(n)
cells$AreaShape_round <- rexp(n)
cells$AreaShape_diameter <- rexp(n, 2)
cells$Intensity_Mean_CD8 <- rexp(n, 10)
cells$Intensity_Mean_CD4 <- rexp(n, 10)

cellExp <- SegmentedCellExperiment(cells, cellProfiler = TRUE)

### Cluster cell types
intensities <- intensity(cellExp)
kM <- kmeans(intensities,2)
cellType(cellExp) <- paste('cluster',kM$cluster, sep = '')

#plot(cellExp, imageID=1)

ellispatrick/SegmentedCellExperiment documentation built on Feb. 24, 2020, 3:14 p.m.