context("test-plotting")
cds <- load_a549()
cds <- estimate_size_factors(cds)
test_that("plot_genes_violin doesn't error", {
cds_subset <- cds[c("ENSG00000228253.1", "ENSG00000103034.14",
"ENSG00000223519.8"),]
plot_genes_violin(cds_subset, group_cells_by="culture_plate")
plot_genes_violin(cds_subset, group_cells_by="culture_plate", pseudocount = 10)
plot_genes_violin(cds_subset, group_cells_by="culture_plate", min_expr = 10)
plot_genes_violin(cds_subset, group_cells_by="culture_plate", ncol=2)
# TO DO
# plot_genes_violin(cds_subset, group_cells_by="culture_plate", color_by = "dose")
plot_genes_violin(cds_subset, group_cells_by="culture_plate", normalize = FALSE)
plot_genes_violin(cds_subset, group_cells_by="culture_plate", log_scale = FALSE)
plot_genes_violin(cds_subset, group_cells_by="culture_plate",
label_by_short_name = FALSE)
# plot_genes_violin(cds_subset, group_cells_by="dose", plot_trend = TRUE,
# ncol = 3)
})
test_that("plot_percent_cells_positive doesn't error", {
cds_subset <- cds[c("ENSG00000228253.1", "ENSG00000103034.14",
"ENSG00000223519.8"),]
plot_percent_cells_positive(cds_subset, group_cells_by="culture_plate")
plot_percent_cells_positive(cds_subset, group_cells_by="culture_plate",
min_expr = 10)
plot_percent_cells_positive(cds_subset, group_cells_by="culture_plate", ncol=2)
plot_percent_cells_positive(cds_subset, group_cells_by="culture_plate",
normalize = FALSE)
plot_percent_cells_positive(cds_subset, group_cells_by="culture_plate",
plot_as_count = TRUE)
plot_percent_cells_positive(cds_subset, group_cells_by="culture_plate",
label_by_short_name = FALSE)
plot_percent_cells_positive(cds_subset, group_cells_by="culture_plate",
plot_limits = c(0,200))
expect_equal(1, 1)
})
test_that("plot_pc_variance_explained doesn't error", {
expect_error(plot_pc_variance_explained(cds),
"Data has not been preprocessed with PCA. Please run preprocess_cds with method = 'PCA' before running plot_pc_variance_explained.")
cds <- preprocess_cds(cds)
plot_pc_variance_explained(cds)
expect_equal(1, 1)
})
test_that("plot_genes_in_pseudotime doesn't error", {
cds_subset <- cds[c("ENSG00000228253.1", "ENSG00000103034.14",
"ENSG00000223519.8"),]
expect_error(plot_genes_in_pseudotime(cds_subset),
"No pseudotime calculated. Must call order_cells first.")
cds <- preprocess_cds(cds)
cds <- reduce_dimension(cds)
cds <- cluster_cells(cds)
cds <- learn_graph(cds)
cds <- order_cells(cds, root_pr_nodes = "Y_1")
cds_subset <- cds[c("ENSG00000228253.1", "ENSG00000103034.14",
"ENSG00000223519.8"),]
plot_genes_in_pseudotime(cds_subset)
plot_genes_in_pseudotime(cds_subset, min_expr = 5)
plot_genes_in_pseudotime(cds_subset, nrow = 5)
plot_genes_in_pseudotime(cds_subset, ncol = 5,
panel_order = c("MT-ATP8", "NDRG4", "KIF28P"))
plot_genes_in_pseudotime(cds_subset, color_cells_by = "culture_plate")
plot_genes_in_pseudotime(cds_subset, label_by_short_name = FALSE)
plot_genes_in_pseudotime(cds_subset, vertical_jitter = 1)
plot_genes_in_pseudotime(cds_subset, horizontal_jitter = 1)
expect_equal(1, 1)
})
test_that("plot_cells doesn't error", {
cds <- preprocess_cds(cds)
plot_cells(cds, reduction_method = "PCA", x=2, y=5)
cds <- reduce_dimension(cds, max_components = 2)
plot_cells(cds)
cds <- cluster_cells(cds)
plot_cells(cds)
cds <- learn_graph(cds)
suppressWarnings(plot_cells(cds))
cds <- order_cells(cds, root_pr_nodes = "Y_1")
plot_cells(cds, color_cells_by = "pseudotime")
plot_cells(cds, color_cells_by = "partition")
plot_cells(cds, color_cells_by = "cluster")
plot_cells(cds, group_cells_by="cluster", color_cells_by="partition")
#plot_cells(cds, group_cells_by="culture_plate", color_cells_by="partition")
plot_cells(cds, genes = c("NDRG4"), min_expr = 1, rasterize = TRUE)
plot_cells(cds, genes = c("NDRG4", "MT-ATP8", "ENSG00000240216.7"))
plot_cells(cds, show_trajectory_graph = FALSE)
plot_cells(cds, trajectory_graph_color = "blue",
trajectory_graph_segment_size = 3)
plot_cells(cds, label_cell_groups = FALSE)
plot_cells(cds, label_groups_by_cluster = FALSE, group_cells_by="partition")
plot_cells(cds, group_label_size = 10)
plot_cells(cds, labels_per_group = 4)
plot_cells(cds, label_branch_points = FALSE, label_roots = FALSE,
label_leaves = FALSE, graph_label_size = 5)
plot_cells(cds, cell_size = 1, alpha = .1)
})
test_that("plot_genes_by_group doesn't error", {
pData(cds)$temp <- c(1,2)
plot_genes_by_group(cds,
c("CPHL1P", "NDRG4",
"HBG2"),
group_cells_by="temp",
ordering_type="maximal_on_diag",
max.size=3)
rowData(cds)$gene_short_name <- NULL
expect_error(plot_genes_by_group(cds,
c("CPHL1P", "NDRG4",
"HBG2"),
group_cells_by="temp",
ordering_type="maximal_on_diag",
max.size=3))
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.