Default to the non-redundant list of elements #' merged from set_1 and set2. #' background The background (universe) to consider. #' The "square" layout shows the hypergeometric pvalue (color) and the Jaccard result (size of the square). Either "raster" (a scatter plot showing the statistics of interest) or "square". #' colors The color palette to be used in the plot. #' transform The transformation to be applied to the values. Note that hypergeometric tests check for enrichment. It can be either "jaccard", "hypergeom", "intersection" #' "size_set_1", "size_set_2", "diff_set_1" (specific to set_1), "diff_set_2" (specific to set_2). #' stat The statistics to be computed between gene sets. #' set_2 A list containing gene sets to be compared. #' #' set_1 A list containing gene sets to be compared. # Compare two lists of gene sets # An internal function to compute p-value # of hypergeometric test hyper_fun <- function ( a, b, N ) # Plot the result of compare_genesets #' Plot the result of compare_genesets #' #' #' This function plots the results of compare_genesets. nclust-ClusterSet-method: Number of clusters in a ClusterSet object.nclust: Number of clusters in a ClusterSet object.mcl_system_cmd: Call MCL program for graph partitioning (internal).lymph_node_selected_spot_2: The lymph_node_selected_spot dataset (#2).lymph_node_selected_spot: The lymph_node_selected_spot dataset.load_example_dataset: Load/download a Visium (10X) example dataset.keep_dbf_graph: Construct a graph based on selected genes in a ClusterSet.grep_clust-ClusterSet-method: Search genes within ClusterSet using a REGEXP.grep_clust: Search genes within ClusterSet using a REGEXP.grapes-in-grapes-character-ClusterSet-method: Match operator of a ClusterSet object.get_verbosity: Get the current verbosity level.get_genes: Extract genes list from each gene clusters.
getFlippedTissueCoordinates: Seurat object internally store spot coordinates (see.get_data_for_scigenex: Fetch an expression matrix from a file, dataframe or Seurat.gene_clustering: Gene clustering using the Markov Cluster Algorithm (MCL).gene_cluster-ClusterSet-method: The gene clusters stored in a ClusterSet.gene_cluster: The gene clusters stored in a ClusterSet.filter_nb_supporting_cells: Filter out cluster supported by few cells.filter_cluster_size: Filter out gene clusters containing few genes.filter_cluster_sd: Filter out gene clusters with small standard deviation.filter_by_dot_prod: Filter cluster from a ClusterSet object using dot product.enrich_go-ClusterSet-method: Enrichment analysis using GO database of gene clusters from a.enrich_go: Enrichment analysis using GO database of gene clusters from a.display_hull: Draw a hull around a region of interest of Visium data.discrete_palette: Generate a discrete color palette.dim-ClusterSet-method: Dimension of a ClusterSet object.create_rand_str: Generate a random string of letters and numbers.create_4_rnd_clust: Generate an example dataset with four clusters of profiles.create_3_rnd_clust: Generate an example dataset with three clusters of profiles.construct_new_graph: Construct a new graph for a ClusterSet object.complex9Noisy: The complex9Noisy dataset A noisy version of the complex9.complex9: The Complex9 dataset A set of 2D points corresponding to 9.compare_genesets: Compare two lists of gene sets.colors_for_gradient: Generate a vector of colors for a gradient.col_names-ClusterSet-method: Column names of a ClusterSet object.clust_size-ClusterSet-method: Sizes of the clusters stored in a ClusterSet object.clust_size: Sizes of the clusters stored in a ClusterSet object.clust_names-ClusterSet-method: The names of the gene clusters stored in the ClusterSet.clust_names: Names of gene clusters stored in the ClusterSet object.cluster_stats-ClusterSet-method: Compute statistics about the clusters.cluster_stats: Compute statistics about the clusters.cluster_set_to_xls-ClusterSet-method: Write Cluster-Set gene lists into an excel sheet.cluster_set_to_xls: Write Cluster-Set gene lists into an excel sheet.cluster_set_from_seurat: Transform a Seurat objects / FindAllMarkers result into a.cluster_set_from_matrix: Transform any matrix and list into a ClusterSet object.check_format_cluster_set: Check the format of a Clusterset object.
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