For classical hierarchical clustering of RNA-seq data, the use of
Euclidean distances as distance metric often result in unnatural
clusters. For example, if the clustering contains genes with only a few
samples with strong up-regulation by hyper-amplifications, these will
weigh heavily at the Euclidean distance(s). This distance metric is
therefore sensitive to outliers. Instead, correlation based clustering
(distance = 1 – correlation(m)) is more common for RNA-seq data, where
spearman’s rank can be used to more aggressively suppress outliers. We
observed some genes, relatively rich in zero counts, of which the
correlation to all other genes are somewhat lower, but the correlations
consistently went in the same direction as other genes within a cluster.
Since the directions of the correlation are consistent with other genes
but the data didn’t seem powerful enough, we took the correlation of the
correlation as the distance metric:
distance = 1 – correlation(correlation(m)). This distance metric was
clustered hierarchically using the “ward.D2”” method, showing neat
natural clusters.
You can install recursiveCorPlot from Github using:
devtools::install_github("yhoogstrate/recursiveCorPlot")Please cite this paper when using recursiveCorPlot for your publications:
Youri Hoogstrate, Kaspar Draaisma, Santoesha A. Ghisai, Levi van Hijfte, Nastaran Barin, Iris de Heer, Wouter Coppieters, Thierry P.P. van den Bosch, Anne Bolleboom, Zhenyu Gao, Arnaud J.P.E. Vincent, Latifa Karim, Manon Deckers, Martin J.B. Taphoorn, Melissa Kerkhof, Astrid Weyerbrock, Marc Sanson, Ann Hoeben, Slávka Lukacova, Giuseppe Lombardi, Sieger Leenstra, Monique Hanse, Ruth E.M. Fleischeuer, Colin Watts, Nicos Angelopoulos, Thierry Gorlia, Vassilis Golfinopoulos, Vincent Bours, Martin J. van den Bent, Pierre A. Robe, Pim J. French,
Transcriptome analysis reveals tumor microenvironment changes in glioblastoma,
Cancer Cell,
2023,
ISSN 1535-6108,
https://doi.org/10.1016/j.ccell.2023.02.019
| Example with G-SAM DE Genes: |
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data('G.SAM.corrected.DE.genes.VST', package = 'recursiveCorPlot') |
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| Above: recursive correlation based clustering |
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| Above: regular 1 - correlation based clustering |
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| Above: scaled Euclidean distance based clustering |