is_errorA: PCA alignment error type A identification and correction

In baumer-lab/cranium: Quantifying Radial Bridge Structures

Description

Identify Error Type A that the y-axis is flipped y-axis and make correction. If the object is brain type (raw data), will perform tidy and PCA reorient functions. If the object is a tbl_brain class (already performed PCA reorientation), will not perform PCA reorientation again.

Usage

is_errorA(data, type = "wildtype", threshold.n = 0.9)

## S3 method for class 'brain'
is_errorA(data, type = "wildtype", threshold.n = 0.9)

## S3 method for class 'tbl_brain'
is_errorA(data, type = "wildtype",
  threshold.n = 0.9)

correct_errorA(data, type = "wildtype", threshold.n = 0.9)

## S3 method for class 'brain'
correct_errorA(data, type = "wildtype",
  threshold.n = 0.9)

correct_errorA(data, type = "wildtype", threshold.n = 0.9)

## S3 method for class 'brain'
correct_errorA(data, type = "wildtype",
  threshold.n = 0.9)

## S3 method for class 'tbl_brain'
correct_errorA(data, type = "wildtype",
  threshold.n = 0.9)

Arguments

data	a brain image
type	wild type or mutant type of zebrafish embryo brain
threshold.n	threshld for signal frequency. Any signal with frequency below threshold value is exluded

Examples

brain <- read_h5(download_brains(tempdir(), pattern = "101"))
is_errorA(brain)
corrected_brain <- correct_errorA(brain)

baumer-lab/cranium documentation built on Nov. 3, 2019, 2:07 p.m.