autoplot() methods for glystats_cc_res and glystats_wgcna_res objects because the corresponding glystats functions have been removed.plot_logo() now fetches protein sequences from Uniprot automatically if a fasta file is not provided.plot_heatmap() cannot handle NA values. Now a more robust clustering method is used and zero-variance variables are removed.plot_volcano() and plot_pca().plot_heatmap() always sends the plot to the plot panel even when the result is passed to a variable.plot_volcano() cannot correctly handle the contrast argument for glystats::gly_limma() results.autoplot() method for glystats::gly_limma() results does not work.plot_volcano() now supports glystats::gly_limma() results with multiple contrasts.pheatmap and ggplotify in plot_heatmap() to plot heatmaps.autoplot() for glystats_wgcna_res objects for now. It will be re-implemented in the future with more features.We redesign most plot_xxx() functions to make them more flexible. Previously, these functions only accepts a glyexp::experiment() object. Now, they also accept corresponding glystats results, to be more intuitive and convenient.
We also redesign the argument passing strategies in plot_xxx() functions, making clear separation between underlying statistical functions and plotting functions.
plot_oplsda() to plot OPLS-DA plot from glyexp::experiment() or glystats::gly_oplsda() results.plot_plsda() to plot PLS-DA plot from glyexp::experiment() or glystats::gly_plsda() results.plot_enrich() to plot dotplot, barplot, or network plot from glyexp::experiment() or glystats enrichment functions (glystats::gly_enrich_go(), glystats::gly_enrich_kegg(), glystats::gly_enrich_reactome()).plot_corrplot() now supports glystats::gly_cor() results.plot_pca() now supports glystats::gly_pca() results.plot_roc() now supports glystats::gly_roc() results.plot_tsne() now supports glystats::gly_tsne() results.plot_umap() now supports glystats::gly_umap() results.plot_volcano() now supports glystats::gly_ttest(), glystats::gly_wilcox(), or glystats::gly_limma() results.stats_args parameter to plot_corrplot(), plot_pca(), plot_roc(), plot_tsne(), plot_umap(), and plot_volcano(), to support specifying arguments for underlying glystats functions.... in all plot_xxx() functions is passed to underlying plotting functions (if any).plot_xxx() functions.plot_xxx() functions.glyexp 0.10.0.test parameter to plot_volcano() to specify the statistical test type.plot_boxplot() to plot grouped boxplots for experiment objects.glystats::gly_roc() results using autoplot() now.plot_roc() to plot ROC curves directly from experiment objects.EnhancedVolcano package.autoplot(). Previously, boxplots were actually plotted when type = "barplot". Now boxplots grouped by the group column are plotted, faceted by variables, when type = "boxplot".rlang::check_installed() for better optional dependency checking.glystats v0.5.0.plot_logo() to plot logo plots for glycosites.autoplot() from ggplot2 to prevent the 'could not find function "autoplot"' error when ggplot2 is not loaded.glyexp v0.8.0.