Man pages for trang1618/tdapseudotime
Temporal Phenotyping via Topological Data Analysis and Pseudo Time
| add_clust_info | Add cluster information |
| centroids | Data frame of centroids, each row represents the mean lab... |
| color_clust | Get cluster colors for nodes. |
| color_graph | Color nodes of graph given coloring method. |
| color_vertex | Adjust colors of nodes using enrichment function. |
| commu_clus | Detect community structure based on edge igraph::betweeness. |
| compute_similarity | Compute similarity based on trajectory |
| convert_id_to_node | Assign observations (ids) to nodes in network. |
| cosine_sim_func | Calculate the pairwise similarity between rows of numeric... |
| find_trajectories | Find trajectories in the MST All the trajectory or choose the... |
| get_graph_properties | Get basic properties of graph |
| make_tda_graph | Make igraph object by calculating adjacency, resizing nodes,... |
| map_tda | Run TDAMapper on a matrix of lab values |
| minspantree | Get minimum spanning tree from graph |
| node_color | Dataframe mapping node to cluster and corresponding color,... |
| out_trajectories | List of trajectories computed from shortest paths. output of... |
| pipe | Pipe operator |
| processed_data | Processed data from sim_dat |
| resize_nodes | Resize the nodes of graph given the number of points it... |
| scaled_lab_mat | Matrix of the scaled lab values of 'sim_dat'. |
| shortest_paths_func | Find the shortest paths. |
| sim_dat | Simulated data from github.com/aridag/TDA_PSEUDOTIME. |
| sim_intersection | Compute intersection similarity to assign each subject to... |
| sim_jaccard | Compute Jaccard similarity to assign each subject to most... |
| sim_length | Compute similarity based on length to assign each subject to... |
| weight_edges | Weight edges of a graph based on mean time of each edge. |
| widen_i2b2 | Convert i2b2 observation dataframe from long to wide. |
