mergeClusters {CATALYST} | R Documentation |
mergeClusters
provides a simple wrapper
to store a manual merging inside the input daFrame
.
mergeClusters(x, table, id) ## S4 method for signature 'daFrame' mergeClusters(x, table, id)
x |
a |
table |
the merging table; a |
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 crowellh@student.ethz.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 lineage <- c("CD3", "CD45", "CD4", "CD20", "CD33", "CD123", "CD14", "IgM", "HLA_DR", "CD7") re <- cluster(re, cols_to_use=lineage) # merge clusters re <- mergeClusters(re, merging_table, "merging") plotClusterHeatmap(re, k="merging", hm2="pS6")