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Fig. 2 | BMC Bioinformatics

Fig. 2

From: pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components

Fig. 2

Selected screenshots of the pcaExplorer application. a Principal components from the point of view of the samples, with a zoomable 2D PCA plot (3D now shown due to space) and a scree plot. Additional boxes show loadings plots for the PCs under inspection, and let users explore the effect of the removal of outlier samples. b Principal components, focused on the gene level. Genes are shown in the PCA plot, with sample labels displayed as in a biplot. A profile explorer and heatmaps (not shown due to space) can be plotted for the subset selected after user interaction. Single genes can also be inspected with boxplots. c Functional annotation of principal components, with an overview of the GO-based functions enriched in the loadings in each direction for the selected PCs. The pca2go object can be provided at launch, or also computed during the exploration. d Report Editor panel, with markdown-related and general options shown. Below, the text editor displays the content of the analysis for building the report, defaulting to a comprehensive template provided with the package

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