plotSpatialPropAll: Plot predicted proportions for all cell types using spatial...

In SpatialDDLS: Deconvolution of Spatial Transcriptomics Data Based on Neural Networks

Plot predicted proportions for all cell types using spatial coordinates of spots

Description

Color spots on the spatial coordinates plot according to their predicted cell type proportions. All cell types are represented together using the same color scale from 0 to 1.

Usage

plotSpatialPropAll(
  object,
  index.st,
  colors = "blues",
  set = "raw",
  prediction = "Regularized",
  size.point = 0.1,
  title = NULL,
  nrow = NULL,
  ncol = NULL,
  theme = NULL
)

Arguments

object	A SpatialDDLS object.
index.st	Index of the spatial transcriptomics data to be plotted. It can be either a position or a name if a named list of SpatialExperiment objects was provided.
colors	Color scale to be used. It can be "blues" or "spectral" (the former by default).
set	If results were simplified (see ?deconvSpatialDDLS for details), which results to plot (raw by default).
prediction	It can be "Regularized", "Intrinsic" or "Extrinsic" ("Regularized" by default).
size.point	Size of points (0.1 by default).
title	Title of plot.
nrow	Number of rows in the split plot.
ncol	Number of columns in the split plot.
theme	ggplot2 theme.

Value

A ggplot object.

See Also

plotSpatialProp deconvSpatialDDLS trainDeconvModel

SpatialDDLS documentation built on Oct. 31, 2024, 5:07 p.m.