Incorporate Bioconductor recommendations #164
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TuomasBorman
commented
Jan 15, 2025
Comment on lines
+547
to
552
| if( add.expl.var && is.null(expl.var) ){ | ||
| eigen_vals <- attr(reduced_dim, "eig") | ||
| # Convert to explained variance and take only first two components | ||
| expl_var <- eigen_vals / sum(eigen_vals) | ||
| expl_var <- expl_var[seq_len(ncomponents)]*100 | ||
| expl_var <- summary(rda)$concont$importance*100 | ||
| } |
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Fixed a bug. First of all, the user can specify explained variance to be plotted with expl.var. That is why it must be NULL in line 547. Moreover, I removed line 561 as it overwrote the calculated variance.
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I went through this PR, and apart from the bug fix described above, this does not change the functionality. It just fixes the coding style. |
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This PR incorporates Bioconductor recommendations for coding practice. It does not modify the functionality.