BrainMap: Internal- Overlaps regional enrichment into a single section

Description Usage Arguments Value Examples

View source: R/BrainMap.R

Description

BrainMap Merges maps from reColor

Usage

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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

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##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.