Changelog

glyvis 0.5.0

New features

• plot_logo() now fetches protein sequences from Uniprot automatically if a fasta file is not provided.

glyvis 0.4.5

Minor improvements and bug fixes

• Fix the bug that plot_heatmap() cannot handle NA values. Now a more robust clustering method is used and zero-variance variables are removed.

glyvis 0.4.4

Minor improvements and bug fixes

• Suppress harmless warnings in plot_volcano() and plot_pca().

glyvis 0.4.3

Minor improvements and bug fixes

• Fix the bug that plot_heatmap() always sends the plot to the plot panel even when the result is passed to a variable.

glyvis 0.4.2

Minor improvements and bug fixes

• Fix the bug that plot_volcano() cannot correctly handle the contrast argument for glystats::gly_limma() results.
• Fix the bug that autoplot() method for glystats::gly_limma() results does not work.

glyvis 0.4.1

Minor improvements and bug fixes

• plot_volcano() now supports glystats::gly_limma() results with multiple contrasts.
• Use pheatmap and ggplotify in plot_heatmap() to plot heatmaps.
• Remove autoplot() for glystats_wgcna_res objects for now. It will be re-implemented in the future with more features.

glyvis 0.4.0

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.

New features

• Add plot_oplsda() to plot OPLS-DA plot from glyexp::experiment() or glystats::gly_oplsda() results.
• Add plot_plsda() to plot PLS-DA plot from glyexp::experiment() or glystats::gly_plsda() results.
• Add 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.
• Add a 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).

Minor improvements and bug fixes

• Add descriptions about supported data types in the documentation of all plot_xxx() functions.
• Fix some inconsistent argument passiing in plot_xxx() functions.

glyvis 0.3.1

Minor improvements and bug fixes

• Fix bugs introduced by the breaking changes in glyexp 0.10.0.

glyvis 0.3.0

New features

• Add a test parameter to plot_volcano() to specify the statistical test type.
• Add plot_boxplot() to plot grouped boxplots for experiment objects.
• ROC curves can be plotted for glystats::gly_roc() results using autoplot() now.
• Add plot_roc() to plot ROC curves directly from experiment objects.

Minor improvements and bug fixes

• Better volcano plots using EnhancedVolcano package.
• Fix the inconsistent behaviour of plotting experiment objects with autoplot(). Previously, boxplots were actually plotted when type = "barplot". Now boxplots grouped by the group column are plotted, faceted by variables, when type = "boxplot".
• Use rlang::check_installed() for better optional dependency checking.

glyvis 0.2.1

Minor improvements and bug fixes

• Adapt to the breaking changes in glystats v0.5.0.

glyvis 0.2.0

New features

• Add plot_logo() to plot logo plots for glycosites.

Minor improvements and bug fixes

• Re-export autoplot() from ggplot2 to prevent the ‘could not find function “autoplot”’ error when ggplot2 is not loaded.
• Add a Get Started vignette.

glyvis 0.1.2

Minor improvements and bug fixes

• Update dependencies to depend on release versions of glycoverse packages.

glyvis 0.1.1

Minor improvements and bug fixes

• Fix bugs in tests introduced by glyexp v0.8.0.

glyvis 0.1.0

• First release.