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R/Utilities.R

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@@ -853,11 +853,10 @@ find_knn_parallel_tree <- function(tree, K) {
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#' Add custom tree based neighbor and weights to a hotspot object
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#' Generate neighbors and weights for a tree object, based on LCA.
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#'
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#' @param tree object of class phylo
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#' @param the hotspot object to add the nw to
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#' @param minSize the minimum number of neighbors of the node
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#' @param minSize the minimum number of neighbors per node
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#' @return the hotspot object
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lcaBasedTreeKNN <- function(tree, minSize=20) {
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tips <- tree$tip.label

R/methods-Module.R

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@@ -748,10 +748,7 @@ draw_hotspot_heatmap <- function(hs, palette = paletteer_d("ggsci::default_nejm"
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example_genes[[mod]] = sample(hs$modules[hs$modules == mod], 5)
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}
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}
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print(module_to_col)
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print(col_mapping[order(names(col_mapping))])
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print(col_mapping)
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print(example_genes)
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modules = data.frame("module" = hs$modules)
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modules$module = as.character(modules$module)
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ha = rowAnnotation(df = modules,

docs/articles/phyloVision.html

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docs/articles/spatialHotspot.html

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docs/articles/trajectories.html

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docs/pkgdown.yml

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@@ -11,7 +11,7 @@ articles:
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web_only/10xData: 10xData.html
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web_only/Seurat: Seurat.html
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web_only/SignatureAutocorrelation: SignatureAutocorrelation.html
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last_built: 2021-06-17T17:55Z
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last_built: 2021-08-19T18:21Z
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urls:
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reference: https://yoseflab.github.io/VISION//reference
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article: https://yoseflab.github.io/VISION//articles

docs/reference/lcaBasedTreeKNN.html

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hotspot_env.yaml

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man/lcaBasedTreeKNN.Rd

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