Load/download a Seurat or ClusterSet example dataset.
load_example_dataset(
dataset = c("7871581/files/pbmc3k_medium", "7871581/files/pbmc3k_medium_clusters",
"8028126/files/pbmc3k_medium_clusters_enr",
"8028226/files/pbmc3k_medium_clusters_enr_sub", "7870305/files/lymph_node_tiny_2",
"7870305/files/lymph_node_tiny_clusters_2", "7869307/files/lymph_node_tiny",
"7869307/files/lymph_node_tiny_clusters"),
timeout = NULL,
force = FALSE
)The name of the dataset.
Set the timout for download (options(timeout=timeout))
Reload the dataset even if already in globalEnv.
Load the dataset.
# An example Seurat/Visium dataset
load_example_dataset("7870305/files/lymph_node_tiny_2")
#> |-- INFO : Dataset 7870305/files/lymph_node_tiny_2 was already loaded.
lymph_node_tiny_2
#> An object of class Seurat
#> 1891 features across 442 samples within 1 assay
#> Active assay: Spatial (1891 features, 2000 variable features)
#> 2 dimensional reductions calculated: pca, umap
#> 1 image present: slice1
# An example clusterSet dataset
load_example_dataset("7870305/files/lymph_node_tiny_clusters_2")
#> |-- INFO : Dataset 7870305/files/lymph_node_tiny_clusters_2 was already loaded.
lymph_node_tiny_clusters_2
#> An object of class ClusterSet
#> Name: f9S1S04hxV
#> Memory used: 7404104
#> Number of cells: 442
#> Number of informative genes: 241
#> Number of gene clusters: 7
#> This object contains the following informations:
#> - data
#> - gene_clusters
#> - top_genes
#> - gene_clusters_metadata
#> - gene_cluster_annotations
#> - cells_metadata
#> - dbf_output
#> - parameters
#> * distance_method = pearson
#> * k = 80
#> * highest = 5e-05
#> * fdr = 0.005
#> * row_sum = 5
#> * no_dknn_filter = FALSE
#> * seed = 123
#> * keep_nn = FALSE
#> * k_mcl_graph = 5
#> * output_path = /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpuPDGyK
#> * name = f9S1S04hxV
#> * inflation = 2.2