plotGiottoImage: Plot a giotto image object

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Plot a giotto image object

Description

Display a giotto image in the viewer panel. Image object to plot can be specified by providing the giotto object containing the image (gobject), the image object name (image_name), and the image object type (image_type). Alternatively, image objects can be directly plotted through their respective associated params.

Usage

plotGiottoImage(
  gobject = NULL,
  image_name = NULL,
  image_type = NULL,
  giottoImage = NULL,
  giottoLargeImage = NULL,
  largeImage_crop_params_list = NULL,
  largeImage_max_intensity = NULL,
  ...
)

Arguments

gobject	gobject containing giotto image object
image_name	name of giotto image object
image_type	type of giotto image object to plot
giottoImage	giottoImage object to plot directly
giottoLargeImage	giottoLargeImage object to plot directly
largeImage_crop_params_list	(optional) named list of params for focusing on a specified region of a giottoLargeImage.
largeImage_max_intensity	(optional) assign override value to treat as maximum intensity in color scale when plotting giottoLargeImage
...	additional params to pass to image object specific plotting functions

largeImage-specific additional params

largeImage_crop_params_list accepts a named list of the following possible params to define a region of interest (ROI) to plot through either a terra extent object OR x and y min and max bounds given as numerics:

• crop_extent – terra extent object to define crop ROI

• xmax_crop – x max of ROI

• xmin_crop – x min of ROI

• ymax_crop – y max of ROI

• ymin_crop – y min of ROI

largeImage_max_intensity accepts a numeric value to set the max value in the plotting color scale. Can be used in case there are high outlier intensity values in the image and a preview with alternative color scaling is desired.

See Also

Other basic image functions: addGiottoImage(), reconnectGiottoImage(), updateGiottoImage()

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