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Preview a Giotto spatial object

plot-generic.Rd

S4 generic for previewing Giotto's image and subcellular objects.

Usage

# S4 method for giottoImage,missing
plot(x, y, ...)

# S4 method for giottoLargeImage,missing
plot(
  x,
  y,
  col,
  max_intensity,
  mar,
  asRGB = FALSE,
  legend = FALSE,
  axes = TRUE,
  maxcell = 5e+05,
  smooth = TRUE,
  ...
)

# S4 method for giottoPolygon,missing
plot(
  x,
  point_size = 0.6,
  type = c("poly", "centroid"),
  max_poly = getOption("giotto.plot_max_poly", 10000),
  ...
)

# S4 method for giottoPoints,missing
plot(x, point_size = 0, feats = NULL, raster = TRUE, raster_size = 600, ...)

# S4 method for spatLocsObj,missing
plot(x, y, ...)

# S4 method for dimObj,missing
plot(x, dims = c(1, 2), ...)

# S4 method for spatialNetworkObj,missing
plot(x, y, ...)

Arguments

x

giotto image, giottoPolygon, or giottoPoints object

y

Not used.

...

additional parameters to pass

col

character. Colors. The default is grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1)

max_intensity

(optional) value to treat as maximum intensity in color scale

mar

numeric vector of length 4 to set the margins of the plot (to make space for the legend). The default is (3, 5, 1.5, 1)

asRGB

(optional) logical. Force RGB plotting if not automatically detected

legend

logical or character. If not FALSE a legend is drawn. The character value can be used to indicate where the legend is to be drawn. For example "topright" or "bottomleft"

axes

logical. Draw axes?

maxcell

positive integer. Maximum number of cells to use for the plot

smooth

logical. If TRUE the cell values are smoothed

point_size

size of points when plotting giottoPoints

type

what to plot: either 'poly' (default) or polygon 'centroid'

max_poly

numeric. If type is not specified, maximum number of polygons to plot before automatically switching to centroids plotting. Default is 1e4. This value is settable using options("giotto.plot_max_poly")

feats

specific features to plot within giottoPoints object (defaults to NULL, meaning all available features)

raster

default = TRUE, whether to plot points as rasterized plot with size based on size param

raster_size

Default is 600. Only used when raster is TRUE

dims

dimensions to plot

Functions

  • plot(x = giottoImage, y = missing): Plot magick-based giottoImage object. ... param passes to .plot_giottoimage_mg

  • plot(x = giottoLargeImage, y = missing): Plot terra-based giottoLargeImage object. ... param passes to .plot_giottolargeimage

  • plot(x = giottoPolygon, y = missing): Plot terra-based giottoPolygon object. ... param passes to plot

  • plot(x = giottoPoints, y = missing): terra-based giottoPoint object. ... param passes to plot

  • plot(x = spatLocsObj, y = missing): Plot a spatLocsObj

  • plot(x = dimObj, y = missing): Plot a dimObj

  • plot(x = spatialNetworkObj, y = missing): Plot a spatialNetworkObj