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

Source: R/plotSpatialCoor.R
plotSpatialPropAll.Rd

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