reColor {brainImageR} | R Documentation

## Color in the brain images based on enrichment values

### 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)

[Package brainImageR version 1.1.0 Index]