| 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")