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Plot a giotto image object

Source: R/images.R
plotGiottoImage.Rd

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

Value

image

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()

Examples

g <- GiottoData::loadGiottoMini("vizgen")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/share/miniconda/envs/giotto_env/bin/python"

plotGiottoImage(g,
    image_type = "largeImage", image_name = "dapi_z0",
    largeImage_max_intensity = 200
)