make.spatial.plot: make.spatial.plot

In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis.

make.spatial.plot

Description

make.spatial.plot

Usage

make.spatial.plot(
  dat,
  image.roi,
  image.channel,
  mask.outlines = NULL,
  cell.dat = NULL,
  cell.col = NULL,
  image.y.flip = TRUE,
  image.mask.size = 0.1,
  image.mask.colour = "gold",
  image.min.threshold = 0,
  image.max.threshold = 0.99,
  image.blank = FALSE,
  cell.x = "x",
  cell.y = "y",
  cell.col.type = "numeric",
  cell.colours = "spectral",
  cell.col.min.threshold = 0.01,
  cell.col.max.threshold = 0.995,
  title = paste0(image.roi),
  dot.size = 1,
  dot.alpha = 1,
  align.xy.by = cell.dat,
  align.col.by = cell.dat,
  save.to.disk = TRUE,
  path = getwd(),
  plot.width = 9,
  plot.height = 7,
  blank.axis = FALSE
)

Arguments

dat	NO DEFAULT.A spatial data list
image.roi	NO DEFAULT.The name of the ROI to plot
image.channel	NO DEFAULT.Name of the channel to plot
mask.outlines	DEFAULT = NULL. Name of the mask for outlines
cell.dat	DEFAULT = NULL. Character name for the cellular dataset in the spatial data list, or a data.table object.
cell.col	DEFAULT = NULL. Name of cellular dataset to colour points by
image.y.flip	DEFAULT = TRUE. Flips the Y-axis orientation.
image.mask.size	DEFAULT = 0.1
image.mask.colour	DEFAULT = "gold"
image.min.threshold	DEFAULT = 0.00. Lower threshold for plot signal. Values below this target will be clipped.
image.max.threshold	DEFAULT = 0.99. Upper threshold for plot signal. Values above this target will be clipped.
image.blank	DEFAULT = FALSE. Will blank the plot image.
cell.x	DEFAULT = "x". Column name for the 'x' coordinate in data.table
cell.y	DEFAULT = "y". Column name for the 'y' coordinate in data.table
cell.col.type	DEFAULT= "numeric". Can be 'factor'.
cell.colours	= DEFAULT = "spectral".
cell.col.min.threshold	= DEFAULT = 0.01. Values below this target will be clipped.
cell.col.max.threshold	= DEFAULT = 0.995. Values above this target will be clipped.
title	DEFAULT = paste0(image.roi)
dot.size	DEFAULT = 1
dot.alpha	DEFAULT = 1
align.xy.by	DEFAULT = cell.dat
align.col.by	DEFAULT = cell.dat
save.to.disk	DEFAULT = TRUE
path	DEFAULT = getwd(). Path for saving image files
plot.width	DEFAULT = 9
plot.height	DEFAULT = 7
blank.axis	DEFAULT = FALSE

ImmuneDynamics/Spectre documentation built on Nov. 12, 2023, 8:12 a.m.