midplane.reflect: Reflect Gene Expression Vector across midplane

In DJFernandes/ABIgeneRMINC: Read, Write, and Analyzing Allen Gene Expression Raw Data

Reflect Gene Expression Vector across midplane

Description

Reflect Gene Expression Vector across midplane

Usage

midplane.reflect(
  gene.expression,
  reflect.dim = NULL,
  minc.array.sizes = NULL,
  data = "gene"
)

Arguments

gene.expression	gene expression data to reflect (as either vector or array)
data	If "gene" (default), then assume missing data has value -1, which is the syntax chosen by ABI for their gene expression data. If "atlas", then missing data is 0, which is the syntax chosen by ABI's for their atlases.
reflect.dimension	INTEGER. Which dimension to reflect. This is done automatically if you use vectors and arrays generated by this package. If you want to do it manually, put 1 for the slowest dimension, 3 for the fastest. To reflect Allen orientation vectors across the sagittal midplane, set this value to 1. To reflect MINC orientation vectors across the sagittal midplane, set this value to 3.
array.dimensions	Vector of length 3 indicating the dimension sizes in order of the SLOWEST dimension to the FASTEST. Must be supplied if gene.expression.vector is missing 'sizes' attributes (execute attr(gene.expression.vector,'sizes')).

Value

Gene Expression as vector or array

Examples

# Read Bdnf gene expression (Experiment 75695642) from Allen Brain Institute
# Look at a coronal slice
# Reflect across the sagittal midplane 
# Look at a coronal slice


## Read Bdnf expression (Experiment 75695642)
URLtoDownload='http://api.brain-map.org/grid_data/download/75695642?include=energy'
gene.expression.vector=read.raw.gene(URLtoDownload,url=TRUE)

## Coronal slice
c.slice=array(gene.expression.vector,rev(attr(gene.expression.vector,'sizes')))[30,,]
image(c.slice, ylab='Left-Right' ,xlab='Superior-Inferior')

## Reflect across the sagittal midplane 
reflected.vector=midplane.reflect(gene.expression.vector,1)

## Coronal slice
reflected.c.slice=array(reflected.vector,rev(attr(gene.expression.vector,'sizes')))[30,,]
image(reflected.c.slice, ylab='Left-Right' ,xlab='Superior-Inferior')

## Reflect MINC orientation vector across sagittal midplane
minc.vector=allenVectorTOmincVector(gene.expression.vector)
reflected.minc.vector=midplane.reflect(minc.vector,3)

DJFernandes/ABIgeneRMINC documentation built on March 21, 2022, 12:05 p.m.