ClassifyReference: Use a reference dataset to classify itself. A good reference...

Description Usage Arguments Value Examples

View source: R/Utils_CHETAH.R

Description

Use a reference dataset to classify itself. A good reference should have almost no mixture between reference cells.

Usage

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ClassifyReference(ref_cells, ref_ct = "celltypes", ref_c = "counts",
  return = FALSE, ...)

Arguments

ref_cells

the reference, similar to CHETAHclassifier's ref_cells

ref_ct

the colData of ref_cells where the cell types are stored.

ref_c

same as input_c, but for the reference.

return

return the matrix that was used to produce the plot

...

Other variables to pass to CHETAHclassifier

Value

A square plot. The rows are the original cell types, the columns the classifion labels. The colors and sizes of the squares indicate which part of the cells of the rowname type are classified to the type of the column name. On the left of the plot, the percentage of cells that is classified to an intermediate type is plotted. A good reference would classify nearly 100

Examples

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CHETAH documentation built on Nov. 8, 2020, 8:02 p.m.