PlotBrain: Color and Plot the SGSE image

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

Description

PlotBrain Plots CreateBrain. The gene set enrichment observe within the microdissected tissues (results of testEnrich) are combined here to show gene set enrichment across broad brain regions. Enriched regions are colored in red, and regions depleted for the query gene list are colored in blue.

Usage

PlotBrain(composite, legend = TRUE)

Arguments

composite	Comp object returned from CreateBrain.
legend	Boolean whether the legend should be included. Default = TRUE

Details

PlotBrain plots your spatial gene set enrichment image.

Value

plots the SGSE brain image

Examples

##First put together a gene list, or load in the default vth dataset
#brainImageR:::loadworkspace()
data(vth)
##Calculate the spatial enrichment.
#composite <- SpatialEnrichment(vth, reps = 20, refset = "developing")
##Calculate the significance of the gene set enrichment
#boot <- testEnrich(composite)
##Color the brain section of interest
#composite <- CreateBrain(composite, boot, slice = 5, pcut = 0.05)
##Plot the brain
#PlotBrain(composite)

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