gene_resample_resolution: Resample gene expression to a different resolution

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

Resample gene expression to a different resolution

Description

Resample gene expression to a different resolution

Usage

gene_resample_resolution(
  gene.expression,
  spacing = NULL,
  interpolation = "cubic"
)

Arguments

gene.expression	Gene expression data read with read.raw.gene (can be 1-D vector or array). If 1-D vector, it must has the sizes attribute
spacing	new resolution to sample either as a vector (one component for each dimension) or scalar. If scalar, new resolution is isotropic.
interpolation	Default is 'cubic'. 'Linear' and 'nearest' are also currently supported.

Value

resampled gene expression

Examples

# read a gene expression file
filename=system.file('extdata/Pdyn_P56_coronal_71717084_200um.zip',package="ABIgeneRMINC")
gene.expression=read.raw.gene(filename)

# convert data from 1-D vector to 3-D array
gene.expression.array=array(gene.expression,rev(attr(gene.expression,'sizes')))
# synonymous with mincArray(gene.expression))

#Sagittal Slice
image(gene.expression.array[,,29], ylab='Superior-Inferior' ,xlab='Anterior-Posterior')
title('Native resolution', font.main=2)

# The current resolution is isotropic 200 microns
attributes(gene.expression)$ANTsRparam$spacing
# 200 200 200

# resample to isotropic 50 microns
resampled.gene.expression = gene_resample_resolution(gene.expression, c(50,50,50))

# The new resolution is
attributes(resampled.gene.expression)$ANTsRparam$spacing
# 50 50 50

# make sagittal slice
resampled.gene.expression.array=array(resampled.gene.expression,rev(attr(resampled.gene.expression,'sizes')))
image(resampled.gene.expression.array[,,29*4], ylab='Superior-Inferior' ,xlab='Anterior-Posterior')
title('4x super-sampling', font.main=2)

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