plotAbundances {CATALYST} | R Documentation |
Plots the relative population abundances of the specified clustering.
plotAbundances( x, k = "meta20", by = c("sample_id", "cluster_id"), group_by = NULL, shape_by = NULL )
x |
|
k |
character string. Specifies which clustering to use. |
by |
a character string specifying whether to plot frequencies by samples or clusters. |
group_by |
a character string. Should corresponds to a column name of
|
shape_by |
a character string. Should correspond to a column name of
|
a ggplot
object.
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) sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md) sce <- cluster(sce) # plot relative population abundances plotAbundances(sce, k="meta12") # ...by sample plotAbundances(sce, k="meta8", by="cluster_id") # ...by cluster