plotSNE {CATALYST} | R Documentation |
t-SNE plot colored by marker expression or clustering.
plotSNE(x, ...) ## S4 method for signature 'daFrame' plotSNE(x, color_by = 20, facet = NULL)
x |
a |
... |
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 |
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)
# 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")