pheatmap2
runs faster than pheatmap
and supports many more distance measures.
It takes the advantage of parallel distance calculation via parallelDist
and fastcluster
packages.
Please install devtools
if you haven't yet.
install.packages("devtools")
Then, you basically install the pheatmap2
package by using:
library(devtools)
install_github("altintasali/pheatmap2")
pheatmap
stands for "Pretty Heatmaps" and it definitely deserves its name. Raivo Kolde, the author of pheatmap
, did an amazing job on heatmap visualization and I strongly believe that pheatmap
is one of the best heatmap tools available. Dave Tang has a really blog post about how to exploit the features of pheatmap, so please check it out.
pheatmap2
adds more features to pheatmap
while keeping its original source code.
- Runs faster
- Distance matrix calculation:
It uses
parallelDist::parDist
function instead ofstats::dist
.parDist
takes the advantage of all available cores on CPU. - Hierarchical clustering:
It uses
fastcluster::hclust
function instead ofstats::hclust
.fastcluster::hclust
is show to perform faster hierarchical clustering thanstats::hclust
- Distance matrix calculation:
It uses
- Supports more distance measures. Here is a list of distance measures (bold text below means also supported by
pheatmap
):- correlation
- euclidean
- maximum
- manhattan
- canberra
- binary
- minkowski
- geodesic
- mahalanobis
- fJaccard
- bhjattacharyya
- bray
- chord
- divergence
- dtw
- hellinger
- kullback
- podani
- soergel
- wave
- whittaker