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PCA plotting function with ggplot2

Source: R/util_PCA_function.R
dot-PCAFunction.Rd

PCA plotting function with ggplot2

Usage

.PCAFunction(
  spe,
  precomputed,
  colourShapeBy,
  selectedVar,
  ROIshapes,
  ROIcolours
)

Arguments

spe

A SpatialExperiment::SpatialExperiment output from standR::readGeoMx()

precomputed

Output from SingleCellExperiment::reducedDim()

colourShapeBy

From input$selected_types

selectedVar

Either "Type" or input$selected_batch

ROIshapes

User input shapes from .PCA_customization() function OR PCA_customization_batch()

ROIcolours

User input colours from .PCA_customization() function OR PCA_customization_batch()

Value

A ggplot2::ggplot2 object

Author

Seung J. Kim