plotSNE {CATALYST}R Documentation

plot t-SNE

Description

t-SNE plot colored by marker expression or clustering.

Usage

plotSNE(x, ...)

## S4 method for signature 'daFrame'
plotSNE(x, color_by = 20, facet = NULL)

Arguments

x

a daFrame.

...

optional arguments.

color_by

numeric value or character string specifying a clustering OR a character string specifying an antibody whose expression to color by.

facet

a character string specifying a factor to subset the data by. One of names(rowData(x)). Defaults to NULL.

Value

a ggplot object.

Author(s)

Helena Lucia Crowell crowellh@student.ethz.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

# construct daFrame
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)

# run t-SNE
re <- tSNE(re, n=50)

# color by clustering
plotSNE(re, color_by=12)

# color by marker expression
plotSNE(re, color_by="pNFkB", facet="condition")


[Package CATALYST version 1.4.2 Index]