BrainMap: Internal- Overlaps regional enrichment into a single section

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

Description

BrainMap Merges maps from reColor

Usage

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

Arguments

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

Value

returns a matrix weighted by the gene overlap

Examples

##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")

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