CreateBrain {brainImageR} | R Documentation |
CreateBrain
convert spatial enrichment into anatomical coordinates.
CreateBrain(composite, boot, slice, pcut = 0.05)
composite |
Comp object returned from SpatialEnrichment |
boot |
result from testEnrich including significance estimates |
slice |
integer brain section |
pcut |
numeric padj filter. |
Comp object
#brainImageR:::loadworkspace() ##First put together a gene list, or load in the default vth dataset data(vth) ##Calculate the spatial enrichment. #composite <- SpatialEnrichment(vth, reps = 20, refset = "developing") #tissueExp1 <- composite@tissueExp1 #random.matrix <- composite@random.matrix ##Calculate the significance estimates #boot <- testEnrich(composite) ##Color the brain section of interest with enrichment #composite <- CreateBrain(composite, boot, slice = 6, pcut = 0.05) ##Plot the brain #PlotBrain(composite, Breaks = 12)