plotSpatialProp: Plot predicted proportions for a specific cell type using...

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

Plot predicted proportions for a specific cell type using spatial coordinates of spots

Description

Color spots on the spatial coordinates according to the predicted proportions of a particular cell type. Color scale is adapted depending on the range of predicted proportions.

Usage

plotSpatialProp(
  object,
  index.st,
  cell.type,
  colors = "blues",
  set = "raw",
  prediction = "Regularized",
  limits = NULL,
  size.point = 1,
  title = 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.
cell.type	Cell type predicted proportions to color spots by.
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), what results to plot (raw by default).
prediction	It can be "Regularized", "Intrinsic" or "Extrinsic" ("Regularized" by default).
limits	A vector of two elements indicating wanted limits for color scale. If NULL (by default), color scale is adjusted to max and min predicted proportions.
size.point	Size of points (0.1 by default).
title	Title of plot.
theme	ggplot2 theme.

Value

A ggplot object.

See Also

plotSpatialPropAll deconvSpatialDDLS trainDeconvModel

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