README.md

In sje30/g2chvc: Analysis files Genes to Cognition Hippocampus vs Cortex project

g2chvc

Genes to Cognition: Hippocampus vs Cortex project. This package provides code relating to our Neural Development article. There is a companion package, g2chvcdata, that stores our data.

Prerequistes

You will first need to install the data package g2chvcdata and the sjemea packages.

Installing this package

To install this package in R you need the devtools package; skip the first line if you already have it installed:

install.packages("devtools")
devtools::install_github("sje30/g2chvc", quick=TRUE)

Setting quick=TRUE prevents the vignettes from being rebuilt (which can take a long time right now.)

Generating the figures

The scripts for generating figures are stored in inst/makefigs/ which you can directly run, e.g.:

require(g2chvc)
source(system.file("makefigs/hvc_rasters.R", package="g2chvc"))

In this case you will see PDFs made in your current working directory. There is one script for each figure in the paper.

Generating the SVM table.

knitr::knit2pdf(system.file("makefigs", "hvc_class.Rnw", package="g2chvc"))

Or from the command line you can do something like:

MC_CORES=8 Rscript -e 'knitr::knit2pdf(system.file("makefigs", "hvc_class.Rnw", package="g2chvc"))'

This will generate a vignette and leave a copy of the .tex file in the /tmp directory and the generated vignette hvc_class.pdf in your working directory.

sje30/g2chvc documentation built on May 30, 2019, 12:04 a.m.