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 = "meta20", facet = c("antigen", "cluster_id"), group_by = "condition", shape_by = NULL)
x |
a |
... |
optional arguments. |
k |
character string. Specifies the clustering to use.
If |
facet |
|
group_by |
character string. Has to appear as a column name of |
shape_by |
character string. Has to appear as 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)
data(PBMC_fs, PBMC_panel, PBMC_md) re <- daFrame(PBMC_fs, PBMC_panel, PBMC_md) # plot median expressions plotMedExprs(re, shape_by = "patient_id") # run clustering re <- cluster(re) # plot median expressions across clusters plotMedExprs(re, facet="cluster_id", k="meta8")