adjclust
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pneuvial
Adjacency-constrained hierarchical clustering of a similarity matrix
This class should probably inherits from `hclust`(and it might simplify some of the functions).
Hi Pierre, Thanks for the developing this package. I have found it really useful for cluttering epigenetic and genetic data. I am currently applying it to large-scale SNP data. I...
According to https://r-pkgs.org/tests.html#test-structure test files in a package should not explicitly load the package. This should be fixed in `adjclust`: ```bash → grep library\(\"adjclust\"\) *.R test_adjclust_equivalentTo_hclust.R:library("adjclust") test_adjclust_equivalentTo_rioja.R:library("adjclust") test_ascendingCompatibility.R:library("adjclust") test_correct.R:library("adjclust") test_corrected_plot.R:library("adjclust")...
``` Call: run.adjclust(mat = mat, type = type, h = h) Cluster method : adjClust Number of objects: 444 ```
Matrices of the class `Matrix::dgCMatrix` are not necessarily symmetric. I do not see any use case of `snpClust` on such matrices: should we drop `snpClust.dgCMatrix`. Note: the `snpStat::ld` function does...
In the heatmaps generated by `plotSim` when a dendrogram is provided, the diagonal elements (= first row in the rotated heatmap) are twice smaller than the other ones. This is...
- [ ] plotSim function - [ ] log option in hicClust - [ ] select function
- [ ] add a feature to choose k or the height directly when dendro is passed - [x] uniform way to handle inputs in all functions (matrices, sparse matrices)...
Nodes label can be added to a dendrogram by setting `nodeLabel=TRUE` in `plot.chac`. Can we add this option to `plotSim` when a dendrogram is provided?