plotMedExprs {CATALYST} | R Documentation |
Plots median marker expressions across samples computed on arcsinh-transformed intensities.
plotMedExprs(x, ...) ## S4 method for signature 'daFrame' plotMedExprs(x, k = 20, facette = c("antigen", "cluster_id"), group_by = "condition")
x |
a |
... |
optional arguments. |
k |
numeric or character string. Specifies the clustering to use.
If |
facette |
|
group_by |
character string. Has to appear as 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) # plot median expressions plotMedExprs(re) # run clustering lineage <- c("CD3", "CD45", "CD4", "CD20", "CD33", "CD123", "CD14", "IgM", "HLA_DR", "CD7") re <- cluster(re, cols_to_use=lineage) # plot median expressions across clusters plotMedExprs(re, facette="cluster_id", k=8)