mergeClusters {CATALYST} | R Documentation |
mergeClusters
provides a simple wrapper
to store a manual merging inside the input daFrame
.
mergeClusters(x, k, table, id) ## S4 method for signature 'daFrame,character,data.frame,character' mergeClusters(x, k, table, id)
x |
a |
k |
a character string specifying the clustering to merge. |
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. |
... |
optional arguments. |
in the following code snippets, x
is a daFrame
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 daFrame
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)
data(PBMC_fs, PBMC_panel, PBMC_md, merging_table) re <- daFrame(PBMC_fs, PBMC_panel, PBMC_md) # run clustering re <- cluster(re) # merge clusters re <- mergeClusters(re, k="meta20", table=merging_table, id="merging") plotClusterHeatmap(re, k="merging", hm2="pS6")