BrainMap {brainImageR} | R Documentation |
BrainMap
Merges maps from reColor
BrainMap(dim, tissueExp, Abrev, Files, slice, refset = c("developing", "adult"))
dim |
numeric dimensions of the original image |
tissueExp |
counts of genes per tissue, from SpatialEnrichment. |
Abrev |
character of all regions in the given section |
Files |
character of tiff images for each region |
slice |
integer of current slice |
refset |
character of reference brain map |
returns a matrix weighted by the gene overlap
##Internal to brainImageR,called within CreateBrain #brainImageR:::loadworkspace() ##First load in a gene set data(vth) ##calculate the spatial enrichment #composite <- SpatialEnrichment(vth, reps = 20, refset = "developing") #tissueExp <- Boot(composite) ##Select the slice of interest #slice <- 4 #Files <- .cache[["EH1434"]][[slice]] #dim <- .cache[["EH1436"]][[slice]] #Select the region of interest #Abrev <- .cache[["EH1438"]] #abrev <- "VZ" # map <- BrainMap(dim = dim , # tissueExp = tissueExp, # Abrev = Abrev, Files = Files, # slice = slice, # refset = "developing")