mergeClusters: Manual cluster merging

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Manual cluster merging

Description

mergeClusters provides a simple wrapper to store a manual merging inside the input SingleCellExperiment.

Usage

mergeClusters(x, k, table, id, overwrite = FALSE)

Arguments

x	a SingleCellExperiment.
k	character string specifying the clustering to merge; valid values are names(cluster_codes(x)).
table	merging table with 2 columns containing the cluster IDs to merge in the 1st, and the cluster IDs to newly assign in the 2nd column.
id	character string used as a label for the merging.
overwrite	logical specifying whether to force overwriting should a clustering with name id already exist.

Details

in the following code snippets, x is a SingleCellExperiment object.

• merging codes are accesible through cluster_codes(x)$id

• all functions that ask for specification of a clustering (e.g. plotAbundances, plotMultiHeatmap) take the merging ID as a valid input argument.

Value

a SingleCellExperiment with newly added cluster codes stored in cluster_codes(.)$id.

Author(s)

Helena L Crowell [e-mail]

References

Nowicka M, Krieg C, Crowell HL, Weber LM et al. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.1)

Examples

# construct SCE & run clustering
data(PBMC_fs, PBMC_panel, PBMC_md, merging_table)
sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
sce <- cluster(sce)

# merge clusters
sce <- mergeClusters(sce, 
  k = "meta20", 
  id = "merging",
  table = merging_table)

# tabulate manual merging
table(cluster_ids(sce, k = "merging"))

# visualize median type-marker expression
plotExprHeatmap(sce, 
  features = "type", 
  by = "cluster_id", 
  k = "merging",
  bars = TRUE)

HelenaLC/CATALYST documentation built on Nov. 30, 2024, 4:04 a.m.