plotAbundances {CATALYST} | R Documentation |
Plots the relative population abundances of the specified clustering.
plotAbundances(x, ...) ## S4 method for signature 'daFrame' plotAbundances(x, k = 20, by = c("sample_id", "cluster_id"), group = NULL)
x |
a |
... |
optional arguments. |
k |
specifies which clustering to use. |
by |
a character string specifying whether to plot frequencies by samples or clusters. |
group |
a character string. Should corresponds to a column name of
|
a ggplot
object.
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) 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) # plot relative population abundances plotAbundances(re, k=12) # ...by sample plotAbundances(re, k=8, by="cluster_id") # ...by cluster