The grammar in one page | Data and mapping | Layers override the plot mapping | Constants are not mappings | Order of layers | Components that are not layers | Labels | Theme | Device-level themes | Scales and legends | Training | Discrete scales | Continuous scales | Fill is its own aesthetic | Legend placement | Positional scales | Facets | Statistical and annotation layers | Bands and reference lines | Heatmaps | Writing your own layer | The base graphics escape hatch | Extending from a package | Combining complete plots | A complete workflow | Inspecting and saving a plot | The contract at a glance | When something goes wrong | Reference | Layers | Known limits

Arguments shared by the image layers | Drawing images at data points | geom_image | geom_image_repel | geom_subview | Sub-views from other graphics systems | Images as backgrounds | geom_bgimage | ggbackground | Images from remote services | geom_pokemon | geom_emoji | geom_icon | geom_flag | geom_worldcup2018 | geom_phylopic | Listing the images that are available | Interactive images | Animating frames with gganimate | What this does not promise | Legend keys | Themes | Reading images | Previewing a plot | The image cache

Interface for dimensionality reduction methods | Visualization | Comparing several methods | Visualizing SingleCellExperiment objects | Clustering and silhouette widths | Method-specific information | Input validation

Theme Elements | Rounded rectangles | Alternating grid bands | Minimal plot backgrounds | Geometric Layers | Histograms based on hist() | X-splines | Continuous-color segments | Shape-like point layers | Facets and Plot Data | Updating facet labels | Extracting mapped data | Legends and Fonts | Summary

Example Data and Differential Analysis | Interactive Volcano Plot Visualization | Point Size Adjustment | FigureYa Themed Volcano Plot | Custom Gene Display and Styles | Highlight Top Significant Genes | Highlight Selected Genes | Pathway Selection and Linked Volcano Explorer

Simple Network Visualization | Node color and size | Node label | Edge | Layouts | Circular Layout | Linear Layout | Network with external data | Network with pies | Category-Item association plot

Introduction | Gap plot | Feature 1: Compatible with ggplot2 | Feature 2: Multiple break-points are supported | Feature 3: Simultaneous breaks on both x and y axes | Feature 4: Axis break symbols | Feature 5: Zoom in or zoom out of subplots | Feature 6: Support reverse scale | Feature 7: Compatible with scale transform functions | Feature 8: Compatible with coord_flip | Feature 9: Compatible with facet_grid and facet_wrap | Feature 10: Compatible with legends | Feature 11: Supports all plot labels | Feature 12: Allows setting tick labels for subplots | Feature 13: Compatible with dual axis | Feature 14: Compatible with patchwork | Feature 15: Axis breaks on a discrete axis | Feature 16: Date and datetime axes | Feature 17: Compatible with ggrepel | Feature 18: Join up a line that crosses a break | Wrap plot | Cut plot | Adjust the amount of space between subplots | Place legend at any position | Note | FAQ

Install package | Introduction | Getting Started Quickly | Supported Analysis | Programmatic Usage | KEGG and COG | eggNOG | Microbe-Disease and Signature Enrichment | Case Study | Data input | Run example | Annotation databases | External data delivery | Session Information

Abstract | Citation | Introduction | ChIP profiling | ChIP peaks coverage plot | Profile of ChIP peaks binding to TSS regions | Heatmap of ChIP binding to TSS regions | Average Profile of ChIP peaks binding to TSS region | Profile of ChIP peaks binding to different regions | Binning method for profile of ChIP peaks binding to TSS regions | Profile of ChIP peaks binding to body regions | Profile of ChIP peaks binding to TTS regions | Peak Annotation | Visualize Genomic Annotation | Visualize distribution of TF-binding loci relative to TSS | Functional enrichment analysis | ChIP peak data set comparison | Profile of several ChIP peak data binding to TSS region | Average profiles | Peak heatmaps | Profile of several ChIP peak data binding to body region | ChIP peak annotation comparision | Functional profiles comparison | Overlap of peaks and annotated genes | Statistical testing of ChIP seq overlap | Shuffle genome coordination | Peak overlap enrichment analysis | Data Mining with ChIP seq data deposited in GEO | GEO data collection | Download GEO ChIP data sets | Overlap significant testing | Need helps? | Session Information | References

Supported file formats | Sequence I/O | FASTA | PHYLIP | CLUSTAL and STOCKHOLM | MEGA | GenBank | Download sequences from NCBI | Format conversion | fasta and phylip conversion | interleaved and sequential format conversion | Sequence manipulation | Filtering, alignment and consensus | Renaming sequences | Summary statistics | Bugs/Feature requests | Session info | References

Overview | Setup | A minimal input object | Build a single pathway plot with pipes | Prepare plotting values with wp_map() | Compare two conditions with wp_comparefill() | Render multiple pathways with wp_render() | A typical analysis pattern | Summary

Features | Enrichment Analysis | Post-hoc Analysis | Utilities | Visualization | Full Vignette | Citation | Need help?

Overview | Scholar IDs | Profile Data | Publications | Citation Histories | Citation Metrics | Publication Details | Comparing Scholars | Coauthor Networks | Journal Rankings | Predicting Future h-index | Formatting Publications for CVs | Mirrors, Retries, and Caching

Overview | Data | Methods | Documentation | Citation | Support

Overview | Supported Data | Supported Analyses | Learn More | Citation | Getting Help

Vignette | Citation | Need helps?

Overview | Supported Analysis | Supported ontologies/pathways | Visualization | Vignette | Citation | Need helps?

emojifont: using emoji font in R | Installation | Emoji characters | Emoji in R plot | base plot | ggplot2 | Emoji in tables | Font Awesome | phylomoji | Limitation | Note | Bugs/Feature requests | Session info

Basic Usage | Deconstructing Layers | 1. The Base Plot | 2. Customizing Edges | 3. Customizing Edge Labels | 4. Customizing Nodes (SNFG Symbols) | 5. Adding Text Labels | Putting It All Together: A Highly Customized Plot | Motif Highlighting

Abstract | Citation | Introduction | Data profiling | Coverage plot | Profile of data in specific regions | Profile of one sample of one reference region | Visualization of base modification | Visualization of gene track | Visualization of motif | Peak Annotation | Visualize Genomic Annotation | Visualize distribution of TF-binding loci relative to TSS | Functional enrichment analysis | ChIP peak data set comparison | ChIP peak annotation comparision | Functional profiles comparison | Overlap of peaks and annotated genes | Statistical testing of ChIP seq overlap | Shuffle genome coordination | Peak overlap enrichment analysis | Data Mining with ChIP seq data deposited in GEO | GEO data collection | Download GEO ChIP data sets | Overlap significant testing | Need helps? | Session Information | References

special note for windows users | meme | The grammar of meme | meme_save: a meme version of ggsave | plot method | + method | multi-language support | grid support | ggplot2 support | cowplot support | font support

Install package | Introduction | Importing MSA data | Basic use: MSA Visualization | Color Schemes | Font | MSA Annotation | Learn more | Session Info

Introduction | Installation | Demonstration | Session information

Introduction | Installation | Run the shiny application | Interactive Web Interface | Tree structure exploration panel | Sample date panel | Temporal signal panel | Phylogenetic signal panel

Introduction | hclust and dendrogram objects | linkage object | agnes, diana and twins objects | pvclust object | Session information

Introduction | Download stats of CRAN packages | Download stats of Bioconductor packages | Shiny apps

Vignette | Citation | Need helps?

Scatter Pie plot | Session info

shadow text grob: shadowtextGrob() and grid.shadowtext() | ggplot2 layer: geom_shadowtext()

grid | ggplot2 | Align plots