Plot a downsampled version of giottoLargeImage. Cropping can increase plot resolution of region of interest.
Usage
.plot_giottolargeimage(
gobject = NULL,
largeImage_name = NULL,
giottoLargeImage = NULL,
crop_extent = NULL,
xmax_crop = NULL,
xmin_crop = NULL,
ymax_crop = NULL,
ymin_crop = NULL,
max_intensity = NULL,
asRGB = FALSE,
stretch = NULL,
axes = TRUE,
smooth = TRUE,
mar = c(3, 5, 1.5, 1),
legend = FALSE,
maxcell = 5e+05,
col = grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1),
asp = 1,
...
)Arguments
- gobject
giotto object
- largeImage_name
name of giottoLargeImage
- giottoLargeImage
giottoLargeImage object
- crop_extent
(optional) extent object to focus on specific region of image
- xmax_crop, xmin_crop, ymax_crop, ymin_crop
(optional) crop min/max x and y bounds
- max_intensity
(optional) value to treat as maximum intensity in color scale
- asRGB
(optional) logical. Force RGB plotting if not automatically detected
- stretch
character. Option to stretch the values to increase contrast: "lin" linear or "hist" (histogram)
- axes
boolean. Default = TRUE. Whether to draw axes
- smooth
boolean. default = TRUE. whether to apply smoothing on the image
- mar
plot margins default = c(3,5,1.5,1)
- legend
whether to plot legend of color scale (grayscale only). default = FALSE
- maxcell
positive integer. Maximum number of image cells to use for the plot
- col
character. Colors for single channel images. The default is grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1). It can also be a data.frame with two columns (value, color) to get a "classes" type legend or with three columns (from, to, color) to get an "interval" type legend
- asp
numeric. (default = 1) specific aspect ratio to use
- ...
additional params to pass to terra::plot or terra::plotRGB depending depending on image type