Plot raw image annotation layer

Usage

plotImage.Region(
  region,
  markers,
  colors = NULL,
  background = "black",
  zoom.level = NULL,
  rescale = list(NULL),
  trim = list(c(0.01, 0.99)),
  window = NULL,
  text_size = 20,
  scalebar = 0,
  gg.output = TRUE,
  bucket = NULL,
  connection = con,
  schema = "CORE_DATA",
  ds = -1,
  ...
)

Arguments

region: A Region object
markers: The markers to plot
colors: The colors to use. Must be same length as markers input
background: Specify the background color (black or white)
zoom.level: Specify a zoom level corresponding to the Enable Visualizer tilebucket. Higher is more zoomed out
rescale: Thresholds for rescaling. Must be given as a list of length-2 vectors of threshold values, min and max, per marker (or NULL, for auto-thresholding) in the form below. If only one list entry is given, it will be applied to all markers uniformly: list( c(min.val, max.val), NULL, ...)
trim: Whether to trim the color scale. Applied after dynamic thresholding. Must be given as a list of length-2 vectors of quantiles, low and high, per marker (or NULL, for no trimming) in the form below. If only one list entry is given, it will be applied to all markers uniformly: list( c(trim.low, trim.high), NULL, ...)
window: Optional filtering by position (0-indexed) in the form: list( c(x_min, x_max), c(y_min, y_max) )
text_size: The text size for the overlay indicating marker colors. This will appear in the bottom right corner of the image. Set to 0 for no text.
scalebar: Length of the scale bar (in microns) to overlay. This will appear in the bottom left corner of the image. Set to 0 for no scale bar.
gg.output: Whether or not to use ggplot2 to render the output. This can be clunky or slow for larger images, which are rastered on the fly.
bucket: Deprecated. Image tiles are now pulled via Portal instead of S3.
connection: The database connection object
schema: The database schema name
ds: A date-stamp of today plus ds (an integer) is used to filter Snowflake queries.
...: Additional arguments

Value

A raster image or ggplot image object, depending on the value passed to gg.output