plotImageMask: Plot pixel content

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Plot pixel content

Description

Visualizes the results of identifyPixelContent().

• plotImageMask(): Distinguishes pixel in back- and foreground. Foreground being the tissue.

• ⁠plotPixelContent():⁠ Visualizes the classification of each pixel in detail.

Usage

plotImageMask(object, ...)

## S4 method for signature 'SPATA2'
plotImageMask(
  object,
  img_name = activeImage(object),
  clr_fg = "black",
  clr_bg = "white"
)

## S4 method for signature 'SpatialData'
plotImageMask(
  object,
  img_name = activeImage(object),
  clr_fg = "black",
  clr_bg = "white"
)

## S4 method for signature 'HistoImage'
plotImageMask(object, clr_fg = "black", clr_bg = "white")

plotPixelContent(object, ...)

## S4 method for signature 'SPATA2'
plotPixelContent(
  object,
  img_name = activeImage(object),
  clrp = "sifre",
  clr_bg = "white",
  clr_fragments = "red",
  clr_tissue = "forestgreen",
  clr_artefact = "blue",
  type = FALSE,
  clrp_adjust = NULL
)

## S4 method for signature 'SpatialData'
plotPixelContent(
  object,
  img_name = activeImage(object),
  clrp = "sifre",
  clr_bg = "white",
  clr_fragments = "red",
  clr_tissue = "forestgreen",
  clr_artefact = "blue",
  type = TRUE,
  clrp_adjust = NULL
)

## S4 method for signature 'HistoImage'
plotPixelContent(
  object,
  clrp = "sifre",
  clr_bg = "white",
  clr_fragments = "red",
  clr_tissue = "forestgreen",
  clr_artefact = "blue",
  type = TRUE,
  clrp_adjust = NULL
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
...	Used to absorb deprecated arguments or functions.
img_name	Character value. The name of the image of interest. If NULL, the active image is chosen by default. Either way, must be one of getImageNames().
clr_fg, clr_bg	Character values. Color with which to display foreground and background of the mask.
clrp	Character value. Specifies the color palette to be used to represent groups of discrete variables. Run validColorPalettes() to obtain valid input options.
clr_artefact, clr_fragments, clr_tissue	Character values. Colors with which to display the content type if type = FALSE.
clrp_adjust	Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.

Value

A ggplot.

Note

Always plots the original justification of the image without transformations.

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.