reColor {brainImageR} | R Documentation |
reColor
quantifies the presence of a gene list within each tissue
reColor(i, slice, tissueExp, dim, Abrev, Files, refset = c("developing", "adult"))
i |
tissue region from within the specified rostral-caudal section |
slice |
current slice |
tissueExp |
tissueExp1 from SpatialEnrichment. |
dim |
Original dimensions of the image |
Abrev |
list of tissue regions |
Files |
list of tiff images |
refset |
reference map. developing (default) or adult |
returns genes counts for each tissue
#brainImageR:::loadworkspace() ##First load a gene set data(vth) ##calculate spatial enrichment #composite <- SpatialEnrichment(vth,20,"developing") #boot <- Boot(composite) #subboot <- c(boot[boot$pvalue < 0.05 & is.finite(boot$FC), "FC"]) #names(subboot) <- rownames(boot[boot$pvalue < 0.05 & is.finite(boot$FC), ]) #tissueExp <- subboot ##Select the slice of interest #slice <- 4 #Files <- .cache[["EH1434"]][[slice]] #dim <- .cache[["EH1436"]][[slice]] ##Select the region of interest #Abrev <- .cache[["EH1438"]][[4]] #abrev <- "VZ" #tmp <- reColor(abrev, slice, tissueExp, dim, Abrev, Files)