plot-SegmentedCells: A basic plot for SegmentedCells object

In spicyR: Spatial analysis of in situ cytometry data

Description

This function generates a basic x-y plot of the location coordinates and cellType data.

Usage

## S4 method for signature 'SegmentedCells,ANY'
plot(x, imageID = NULL)

Arguments

x	A SegmentedCells 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 <- SegmentedCells(cells, cellProfiler = TRUE)

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

#plot(cellExp, imageID=1)

spicyR documentation built on March 17, 2021, 6:01 p.m.