Fix slow distance matrix calculation #1154
Open
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Distance matrix calculation is extremely slow when using correlation-based distance and NAs are present. The existing strategy utilizes nested for loops via the ComplexHeatmap:::dist2 function when NAs are present in the matrix. This solution is too slow for large matrices (e.g., 10000 x 100). These nested for loops can be avoided by using the use = "pairwise.complete.obs" argument of the stats::cor function yielding quick distance matrix calculation in the presence of NAs.