augmentCordinateFeatures: Augment all features involving locations

In nbenn/singleCellFeatures: Analyze single cell features stored in an openBIS instance

Description

All features containing the strings "Location_Center_X" or "Location_Center_Y" are extended to include their membership to an ellipse ( concentric w.r.t. image center/well center), their membership to a tile (at well and image level), the number of nonempty neighbor tiles, the type of tile (inwards/outwards facing image border/edge) the distance to the image/ well center, the local object density to the image center. If features labelled with "Location_Shifted_X" or "Location_Shifted_Y" are present (augmentImageLocation), Those are extended too.

Usage

augmentCordinateFeatures(x, ...)

Arguments

x	The PlateData/WellData/ImageData object of interest.
ellipse	An integer corresponding to the number of ellipses.
facet	A vector of length 2 e.g. c(14, 10) corresponding to the number of bins in x-direction (14) and y-direction (10).
center.dist	Logical, whether to include distances to image/well centers.
density	Logical, whether to estimate densities.

Value

The augmented version of the original object.

Examples

data <- PlateData(PlateLocation("J101-2C"))
aug <- augmentCordinateFeatures(data, 5, c(14, 10), TRUE, TRUE)

nbenn/singleCellFeatures documentation built on May 23, 2019, 12:24 p.m.