plotFeatureMatrix: Plot a matrix of pairwise shape/size feature of nuclei...

In karenkuang37/MyoManager: Visual analysis of skeletal muscle microscopy data

Description

The following function plots a matrix of pairwise scatter plots and density distribution of the four shape/size features of cell nuclei computed from getFeatureData(): area, perimeter, radius, and eccentricity. Correlation value of the four features is also calculated.

Usage

plotFeatureMatrix(featureDF)

Arguments

featureDF

A data frame containing four columns of shape/size features for each nuclei objects in an Image.

Value

A matrix composed of pairwise scatter plots, density distribution, and correlation values of the four shape/size features of cell nuclei.

References

Gregoire Pau, Florian Fuchs, Oleg Sklyar, Michael Boutros, and Wolfgang Huber (2010): EBImage - an R package for image processing with applications to cellular phenotypes. Bioinformatics, 26(7), pp. 979-981, link https://bioconductor.org/packages/release/bioc/html/EBImage.html

Examples

# Example 1
rabbit = loadImage(system.file('extdata/Rabbit_01.tif', package='MyoManager'))
rNuc = selectFrame(rabbit, 3)
rNuc_df = getFeatureData(rNuc)
plotFeatureMatrix(rNuc_df)

# Example 2
mouse = loadImage(system.file('extdata/Mouse_01.tiff', package='MyoManager'))
mNuc = selectFrame(mouse, 3)
mNuc_df = getFeatureData(mNuc)
plotFeatureMatrix(mNuc_df)

karenkuang37/MyoManager documentation built on Dec. 21, 2021, 5:18 a.m.