Suggested addition: a PCA illustrating sample/condition/replicates

Description of feature

Maybe this isn't the typical case for most users, but my experiment has multiple replicates of treatment and control. If I wanted to check how concordant my replicates were, and how separated my treatment from control conditions were, I'd likely attempt a PCA based on the raw or normalized counts produced by MAGeCK, coloring the points both by sample and condition (similar to DESeq2 output in nf-core/rnaseq). This could also help identify whether any sample(s) were outliers compared to others, which would be supported by the countsummary table--ie perhaps one sample was an outlier from others in PC space and also has a lower-than-usual mapping rate or very high Gini index etc.

I'd also plot the cross-sample pairwise correlations of normalized counts as a (n * n) heatmap, which likely also would be a useful output

Review the existing MAGeCK outputs, especially the countsummary table, and compare the requested quality-control presentation with the DESeq2 example in the linked nf-core/rnaseq documentation. Define the PCA colored by sample and condition and the normalized-count correlation heatmap, with completion marked by both plots being available as pipeline outputs and supporting replicate and outlier assessment.