plot,SegmentedCells,ANY-method {spicyR} | R Documentation

## A basic plot for SegmentedCells object

### 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)

[Package spicyR version 1.2.1 Index]