Plot the cell-type fractions in your simulated dataset
Examples
counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol=300), sparse = TRUE)
tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol=300), sparse = TRUE)
tpm <- Matrix::t(1e6*Matrix::t(tpm)/Matrix::colSums(tpm))
colnames(counts) <- paste0("cell_",rep(1:300))
colnames(tpm) <- paste0("cell_",rep(1:300))
rownames(counts) <- paste0("gene_",rep(1:1000))
rownames(tpm) <- paste0("gene_",rep(1:1000))
annotation <- data.frame("ID"=paste0("cell_",rep(1:300)),
"cell_type"=c(rep("T cells CD4",50),
rep("T cells CD8",50),
rep("Macrophages",100),
rep("NK cells",10),
rep("B cells",70),
rep("Monocytes",20)))
dataset <- SimBu::dataset(annotation = annotation,
count_matrix = counts,
tpm_matrix = tpm,
name = "test_dataset")
#> Filtering genes...
#> Created dataset.
s <- SimBu::simulate_bulk(dataset,
scenario="even",
scaling_factor="NONE",
nsamples=10,
ncells=100)
#> Finished simulation.
SimBu::plot_simulation(s)
#> Error in rgb(c(166, 31, 178, 51, 251, 227, 253, 255, 202), c(206, 120, 223, 160, 154, 26, 191, 127, 178), c(227, 180, 138, 44, 153, 28, 111, 0, 214), maxColorValue = 255): could not find function "rgb"