Spatial cellular neighbourhood scanning in R
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Documentation for package ‘hoodscanR’ version 1.3.3
Help Pages
| calcMetrics | Calculate metrics for probability matrix |
| clustByHood | Cluster the probability matrix with K-means |
| clustByHood-method | Cluster the probability matrix with K-means |
| findNearCells | Find the k-th nearest cells for each cell |
| mergeByGroup | Merge probability matrix based on annotations |
| mergeHoodSpe | Merge probability matrix into SpatialExperiment object. |
| perplexityPermute | Compute p-value for perplexity via permutation |
| plotColocal | Plot heatmap for neighbourhood analysis |
| plotColocal-method | Plot heatmap for neighbourhood analysis |
| plotHoodMat | Plot probability matrix as a heatmap |
| plotHoodMat-method | Plot probability matrix as a heatmap |
| plotProbDist | Plot probability distribution |
| plotProbDist-method | Plot probability distribution |
| plotTissue | Plot cells based on cell position on tissue. |
| readHoodData | Read cellular position and annotation data into a list object. |
| scanHoods | Scan cellular neighbourhoods. |