Preview a Giotto spatial object — plot-generic • GiottoClass

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

Usage

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

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

# S4 method for class 'giottoAffineImage,missing'
plot(x, y, ...)

# S4 method for class 'giottoPolygon,missing'
plot(
  x,
  point_size = 0.6,
  type = c("poly", "centroid"),
  max_poly = getOption("giotto.plot_max_poly", 1e+06),
  ...
)

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

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

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

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

# S4 method for class 'affine2d,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 raster_size param. See details. When FALSE, plots via terra::plot()
raster_size: Default is 600. Only used when raster is TRUE
dims: dimensions to plot

Value

plot

Details

[giottoPoints raster plotting] Fast plotting of points information by rasterizing the information using terra::rasterize(). For terra SpatVectors, this is faster than scattermore plotting. When plotting as a raster, col colors map on whole image level, as opposed to mapping to individual points, as it does when raster = FALSE Allows the following additional params when plotting with no specific feats input:

force_size logical. raster_size param caps at 1:1 with the spatial extent, but also with a minimum resulting px dim of 100. To ignore these constraints, set force_size = FALSE
dens logical. Show point density using count statistic per rasterized cell. (Default = FALSE). This param affects col param is defaults. When TRUE, col is grDevices::hcl.colors(256). When FALSE, "black" and "white" are used.
background (optional) background color. Usually not used when a col color mapping is sufficient.

Note that col param and other base::plot() graphical params are available through ...

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
plot(x = affine2d, y = missing): Plot a affine2d. blue is start, red is end

Examples

######### giottoLargeImage plotting #########
if (FALSE) { # \dontrun{
gimg <- GiottoData::loadSubObjectMini("giottoLargeImage")
gimg <- GiottoClass:::.update_giotto_image(gimg) # only needed if out of date
plot(gimg)
plot(gimg, col = grDevices::hcl.colors(256))
plot(gimg, max_intensity = 100)
} # }

######### giottoPolygon plotting #########
gpoly <- GiottoData::loadSubObjectMini("giottoPolygon")
plot(gpoly)

plot(gpoly, type = "centroid")


######### giottoPoints plotting #########
gpoints <- GiottoData::loadSubObjectMini("giottoPoints")

# ----- rasterized plotting ----- #
# plot points binary
plot(gpoints)

# plotting all features maps colors on an image level
plot(gpoints, col = grDevices::hcl.colors(n = 256)) # only 2 colors are used

plot(gpoints, col = "green", background = "purple")


# plot points density (by count)
plot(gpoints, dens = TRUE, raster_size = 300)


# force_size = TRUE to ignore default constraints on too big or too small
# (see details)
plot(gpoints, dens = TRUE, raster_size = 80, force_size = TRUE)


# plot specific feature(s)
plot(gpoints, feats = featIDs(gpoints)[seq_len(4)])


# ----- vector plotting ----- #
# non-rasterized plotting (slower, but higher quality)
plot(gpoints, raster = FALSE)


# vector plotting maps colors to transcripts
plot(gpoints, raster = FALSE, col = grDevices::rainbow(nrow(gpoints)))


# plot specific feature(s)
plot(gpoints, feats = featIDs(gpoints)[seq_len(4)], raster = FALSE)


######### spatLocsObj plotting #########
sl <- GiottoData::loadSubObjectMini("spatLocsObj")
plot(sl)


######### dimObj plotting #########
d <- GiottoData::loadSubObjectMini("dimObj")
plot(d)

plot(d, dims = c(3, 5))