plot,SegmentedCells,ANY-method | R Documentation |
This function generates a basic x-y plot of the location coordinates and cellType data.
## S4 method for signature 'SegmentedCells,ANY'
plot(x, imageID = NULL)
x |
A SegmentedCells object. |
imageID |
The image that should be plotted. |
A ggplot object.
'plot(x, imageID = NULL)'
### 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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.