mergeClusters {CATALYST} | R Documentation |
mergeClusters
provides a simple wrapper to
store a manual merging inside the input SingleCellExperiment
.
mergeClusters(x, k, table, id)
x |
|
k |
a character string specifying the clustering to merge.
Should be one of |
table |
a 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. |
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
, plotClusterHeatmap
)
take the merging ID as a valid input argument.
Writes the newly assigend cluster codes into
the metadata slot cluster_codes
of the input
SingleCellExperiment
and returns the latter.
Helena Lucia Crowell helena.crowell@uzh.ch
Nowicka M, Krieg C, 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)
# 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", table=merging_table, id="merging") plotClusterHeatmap(sce, k="merging", hm2="pS6")