reColor: Color in the brain images based on enrichment values

In saralinker/brainImageR: A Framework for visualizing gene set enrichment throughout neurodevelopment

Description

reColor quantifies the presence of a gene list within each tissue

Usage

reColor(i, slice, tissueExp, dim, Abrev, Files, refset = c("developing",
  "adult"))

Arguments

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

Value

returns genes counts for each tissue

Examples

#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)

saralinker/brainImageR documentation built on May 29, 2019, 1:51 p.m.