Man pages for huqiwen0313/speciesTree
Tree based method for cross-species integration
| AddTreeAttribute | Add attribute into the tree |
| AllUpperLevelInfo | Get all upperlevel annotations concanated with "+" |
| assign_values_to_nodes | assign attribute value to dendrogram |
| bestClusterTreeThresholds | caculate jacard coefficiency from best maching tree |
| buildSpeciesTree | build entire tree based on dendrogram and subsampled... |
| clusterMappingSummary | cross-species mapping summary: 1:1, or many:many |
| cluster.matrix.expression.distances | Evaluate expression distances between clusters |
| dendSetColor2factorNormMixing | colored tree by species mixing based on normalized value -... |
| dendSetColorByMixing | Color tree based on mixing of species - unnormalized |
| dendSetColorByNormMixing | colored tree by species mixing based on normalized value |
| dendSetWidthBysize | Set width of tree base on size of clusters |
| getLeafcontent | get leaf information from igraph obj |
| getLeafcontentFlat | get leaf information from cell annotation |
| getUpperLevelNode | get highest node with upperlevel information |
| hello | Hello, World! |
| mappingLabel | mapping leaf node according to cell annotation |
| MarkMixedNode | caculate branch entropy attribute for normalized value |
| NormTree | normalize to upperlevel |
| NormTreeWithinFactor | Normalize tree based on within-factors |
| plot3factorLengend | plot 3-factor legend |
| plotStability | visulize stability measurements of leaf nodes |
| pruneTree | prune tree based on mixing |
| pruneTreeEntropy | prune tree based on entropy |
| rleiden.detection | Run recursive leiden clustering algorithm - modified from... |
| subSampleTree | generate subsampled dendrograms from gene expression matrix |
| subSamplingGraph | subsampling graph |
| TransferDend | Change the format of tree |
| transferLeaflabel | mapping leaf cells to cell annotation |
| TreeEntropy | caculate branch entropy attribute for normalized value |
| TreeStability | return stability scores for each node by searching for... |
| TreeStabilityDend | caculate stability only based on dendrogram and subsampled... |
| UpperLevelInfo | add upperlevel attributes into the tree |
