runCPie {SpatialCPie} | R Documentation |
Runs the SpatialCPie gadget.
runCPie(counts, image = NULL, spotCoordinates = NULL, margin = "spot", resolutions = 2:4, assignmentFunction = function(k, x) kmeans(x, centers = k)$cluster, view = NULL)
counts |
gene count matrix or a
|
image |
image to be used as background to the plot. |
spotCoordinates |
|
margin |
which margin to cluster. |
resolutions |
|
assignmentFunction |
function to compute cluster assignments. |
view |
|
a list with the following items:
"clusters"
: Cluster assignments (may differ from assignments
)
"treePlot"
: The cluster tree ggplot object
"piePots"
: The pie plot ggplot objects
if (interactive()) { options(device.ask.default = FALSE) ## Set up coordinate system coordinates <- as.matrix(expand.grid(1:10, 1:10)) ## Generate data set with three distinct genes generated by three ## distinct cell types profiles <- diag(rep(1, 3)) + runif(9) centers <- cbind(c(5, 2), c(2, 8), c(8, 2)) mixes <- apply(coordinates, 1, function(x) { x <- exp(-colSums((centers - x) ^ 2) / 50) x / sum(x) }) means <- 100 * profiles %*% mixes counts <- matrix(rpois(prod(dim(means)), means), nrow = nrow(profiles)) colnames(counts) <- apply( coordinates, 1, function(x) do.call(paste, c(as.list(x), list(sep = "x"))) ) rownames(counts) <- paste("gene", 1:nrow(counts)) ## Run SpatialCPie runCPie(counts) }