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GenerateLabels

Generates cellular phenotype labels


Description

GenerateLabels returns a list of cell type and cell state labels, as well as novel cellular phenotypes and unclassified cells.

Usage

GenerateLabels(
  cr,
  E = NULL,
  smooth = TRUE,
  new_populations = NULL,
  new_categories = NULL,
  min.cells = 10,
  spring.dir = NULL
)

Arguments

cr

list returned by Signac or by SignacFast.

E

a sparse gene (rows) by cell (column) matrix, or a Seurat object. Rows are HUGO symbols.

smooth

if TRUE, smooths the cell type classifications. Default is TRUE.

new_populations

Character vector specifying any new cell types that were learned by Signac. Default is NULL.

new_categories

If new_populations are set to a cell type, new_category is a corresponding character vector indicating the population that the new population belongs to. Default is NULL.

min.cells

If desired, any cell population with equal to or less than N cells is set to "Unclassified." Default is 10 cells.

spring.dir

If using SPRING, directory to categorical_coloring_data.json. Default is NULL.

Value

A list of cell type labels for cell types, cell states and novel populations.

Examples

## Not run: 
# download single cell data for classification
file.dir = "https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_v3/"
file = "pbmc_1k_v3_filtered_feature_bc_matrix.h5"
download.file(paste0(file.dir, file), "Ex.h5")

# load data, process with Seurat
library(Seurat)
E = Read10X_h5(filename = "Ex.h5")
pbmc <- CreateSeuratObject(counts = E, project = "pbmc")

# run Seurat pipeline
pbmc <- SCTransform(pbmc, verbose = FALSE)
pbmc <- RunPCA(pbmc, verbose = FALSE)
pbmc <- RunUMAP(pbmc, dims = 1:30, verbose = FALSE)
pbmc <- FindNeighbors(pbmc, dims = 1:30, verbose = FALSE)

# download bootstrapped reference data for training models
file.dir = "https://github.com/mathewchamberlain/Signac/blob/master/data/"
file = "training_HPCA.rda"
download.file(paste0(file.dir, file, "?raw=true"), destfile = "training_HPCA.rda")
load("training_HPCA.rda")

# classify cells
labels = SignacFast(E = pbmc, R = training_HPCA)
celltypes = GenerateLabels(labels, E = pbmc)

## End(Not run)

SignacX

Cell Type Identification and Discovery from Single Cell Gene Expression Data

v2.2.0
GPL-3
Authors
Mathew Chamberlain [aut, cre], Virginia Savova [aut], Richa Hanamsagar [aut], Frank Nestle [aut], Emanuele de Rinaldis [aut], Sanofi US [fnd]
Initial release
2021-02-24

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