plot,SegmentedCells,ANY-method {spicyR} | 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)