reColor: Color in the brain images based on enrichment values

Description Usage Arguments Value Examples

View source: R/reColor.R

Description

reColor quantifies the presence of a gene list within each tissue

Usage

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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

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#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)

brainImageR documentation built on May 6, 2019, 3:54 a.m.