plot_mds {CytoGLMM} | R Documentation |
MDS on median marker expression
plot_mds( df_samples, protein_names, sample_info_names, color, sample_label = "" )
df_samples |
Data frame or tibble with proteins counts, cell condition, and group information |
protein_names |
A vector of column names of protein to use in the analysis |
sample_info_names |
Column names that contain information about the cell, e.g. donor, condition, file name, or cell type |
color |
Column name |
sample_label |
Column name |
cowplot
object
set.seed(23) df <- generate_data() protein_names <- names(df)[3:12] df <- dplyr::mutate_at(df, protein_names, function(x) asinh(x/5)) CytoGLMM::plot_mds(df, protein_names = protein_names, sample_info_names = c("donor", "condition"), color = "condition")