SpaCET.visualize.spatialFeature: Spatial feature visualization

In data2intelligence/SpaCE: Spatial Cellular Estimator for Tumors

Spatial feature visualization

Description

Visualize multiple types of spatial features in ST data.

Usage

SpaCET.visualize.spatialFeature(
  SpaCET_obj,
  spatialType = c("QualityControl", "GeneExpression", "CellFraction", "LRNetworkScore",
    "Interface", "GeneSetScore"),
  spatialFeatures = NULL,
  scaleTypeForGeneExpression = "LogTPM",
  sameScaleForFraction = FALSE,
  colors = NULL,
  pointSize = 1,
  nrow = 1,
  imageBg = TRUE,
  interactive = FALSE
)

Arguments

SpaCET_obj	An SpaCET object.
spatialType	Type of spatial features, i.e., "QualityControl", "GeneExpression", "CellFraction", "LRNetworkScore", "Interface", and "GeneSetScore". See ‘details’ for more information.
spatialFeatures	A vector of spatial features.
scaleTypeForGeneExpression	Scale type of gene expression, i.e., "RawCounts","LogRawCounts","LogTPM/10", and "LogTPM".
sameScaleForFraction	Indicate whether all cell types have the same scale for cell fraction.
nrow	Row number of the combined panel for multiple spatial features.
imageBg	logical: should the image be shown?

Details

'SpaCET.visualize.spatialFeature' is able to plot multiple types of spatial features, including "QC", "GeneExp", "CellFraction", and "LRNetworkScore". "QualityControl" refers to quality control metrics. User can visualize the total counts of UMI and genes across all spots. "GeneExpr" is set to visualize the expression level of genes. "CellFraction" refers to the cell fraction of cell types. "LRNetworkScore" is selected to show the Ligand-Receptor network score. See 'SpaCET.CCI.LRNetworkScore' for how to calculate it.

Value

A ggplot2 object.

Examples

SpaCET.visualize.spatialFeature(SpaCET_obj, spatialType = "QualityControl", spatialFeatures=c("UMI","Gene"))
SpaCET.visualize.spatialFeature(SpaCET_obj, spatialType = "GeneExpression", spatialFeatures=c("EPCAM","MS4A1"))
SpaCET.visualize.spatialFeature(SpaCET_obj, spatialType = "CellFraction", spatialFeatures=c("Malignant","Macrophage"))
SpaCET.visualize.spatialFeature(SpaCET_obj, spatialType = "CellFraction", spatialFeatures="All", pointSize = 0.1, nrow=5)
SpaCET.visualize.spatialFeature(SpaCET_obj, spatialType = "LRNetworkScore", spatialFeatures=c("Network_Score","Network_Score_pv"))

data2intelligence/SpaCE documentation built on April 6, 2024, 2:32 a.m.