distGiottoImage: Plot distribution of image intensity values

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Plot distribution of image intensity values

Description

Plot distribution of intensity values using either a density plot or a histogram. Useful for finding image artefact outliers and determining reasonable scaling cutoffs.

Usage

distGiottoImage(
  gobject = NULL,
  image_type = "largeImage",
  image_name = NULL,
  giottoLargeImage = NULL,
  method = c("dens", "hist")
)

Arguments

gobject	giotto object
image_type	image object type (only supports largeImage and is set as default)
image_name	name of image object to use
giottoLargeImage	giotto large image object
method	plot type to show image intensity distribution

Details

Plot is generated from a downsampling of the original image

Plotting method 'dens'

Density plot of intensity values for image objects. N total values examined. Bandwidth refers to the curve smoothing value applied.

Plotting method 'hist'

Histogram of intensity values for image objects.

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.