plotMedExprs {CATALYST}R Documentation

Plot median expressions

Description

Plots median marker expressions across samples computed on arcsinh-transformed intensities.

Usage

plotMedExprs(x, ...)

## S4 method for signature 'daFrame'
plotMedExprs(x, k = "meta20", facet = c("antigen",
  "cluster_id"), group_by = "condition", shape_by = NULL)

Arguments

x

a daFrame.

...

optional arguments.

k

character string. Specifies the clustering to use. If facet = "antigen", this argument will be ignored.

facet

"antigen" or "cluster_id". Note that the latter requires having run cluster first.

group_by

character string. Has to appear as a column name of rowData(x). Specifies a factor to group samples by.

shape_by

character string. Has to appear as a column name of rowData(x). Specifies a factor to shape by.

Value

a ggplot object.

Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

References

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)

Examples

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")


[Package CATALYST version 1.8.7 Index]