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make.spatial.plot

Source: R/make.spatial.plot.R
make.spatial.plot.Rd

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