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Add pkgdown dark theme and improve vignette eval guards
- Add _pkgdown.yml with echoverse dark theme (bslib + custom CSS) - Organize 48 exports into 9 reference groups - Add has_internet guards to vignette chunks that download data - Keep eval=FALSE for expensive external API calls (annotate_snps) - Fix VignetteIndexEntry in cell_type_specific_epigenomics - Add curl to Suggests for connectivity check Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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‎DESCRIPTION‎

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IRanges,
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rlang
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Suggests:
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curl,
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XGR,
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markdown,
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rmarkdown,

‎_pkgdown.yml‎

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url: https://rajlabmssm.github.io/echoannot/
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template:
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bootstrap: 5
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bslib:
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bg: "#1a2744"
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fg: "#e8f4f4"
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primary: "#4ecdc4"
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secondary: "#3a8d8c"
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success: "#2ee8d6"
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info: "#5bc0be"
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code-bg: "#d6e4ee"
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code-color: "#1a2744"
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border-color: "#2a4060"
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link-color: "#4ecdc4"
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link-hover-color: "#2ee8d6"
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font-size-base: "1rem"
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includes:
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in_header: |
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<style>
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.navbar {
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background-color: #162038 !important;
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border-bottom: 2px solid #4ecdc4;
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}
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.navbar-brand, .nav-link { color: #e8f4f4 !important; }
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.nav-link:hover { color: #2ee8d6 !important; }
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.nav-link.active { color: #2ee8d6 !important; border-bottom: 2px solid #2ee8d6; }
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pre {
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background-color: #d6e4ee !important;
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color: #1a2744 !important;
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border: none !important;
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border-radius: 12px;
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margin: 0;
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padding: 0.8em 1em;
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}
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code { color: #1a6b68 !important; border: none !important; }
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pre code { color: #1a2744 !important; border: none !important; background: transparent !important; }
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pre code span { border: none !important; background: transparent !important; }
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.table { color: #e8f4f4 !important; }
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.table-striped > tbody > tr:nth-of-type(odd) > * {
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background-color: rgba(78, 205, 196, 0.05) !important;
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color: #e8f4f4 !important;
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}
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.table-striped > tbody > tr:nth-of-type(even) > * {
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background-color: transparent !important;
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color: #e8f4f4 !important;
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}
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.table > thead { border-bottom: 2px solid #4ecdc4; }
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h1, h2, h3, h4, h5, h6 { color: #4ecdc4 !important; }
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a { color: #5bc0be; }
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a:hover { color: #2ee8d6; }
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.card { background-color: #1e3050; border-color: #2a4060; }
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.footer { background-color: #162038 !important; border-top: 1px solid #2a4060; }
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.page-header { border-bottom: 2px solid #3a8d8c; }
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.sourceCode {
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background-color: #d6e4ee !important;
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border: 1px solid #3a8d8c;
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border-radius: 12px !important;
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overflow: hidden;
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}
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.sourceCode code span,
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.sourceCode code a {
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border: none !important;
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outline: none !important;
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box-shadow: none !important;
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background: transparent !important;
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}
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</style>
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navbar:
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structure:
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left: [intro, reference, articles, news]
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right: [search, github]
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components:
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github:
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icon: fa-github
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href: https://github.com/RajLabMSSM/echoannot
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articles:
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- title: Getting started
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contents:
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- echoannot
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- title: Epigenomics
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contents:
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- cell_type_specific_epigenomics
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reference:
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- title: Annotation functions
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desc: Annotate SNPs with functional information
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contents:
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- annotate_snps
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- annotate_missense
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- annotation_file_name
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- title: NOTT2019 data
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desc: Brain cell-type-specific epigenomic data from Nott et al. 2019
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contents:
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- NOTT2019_epigenomic_histograms
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- NOTT2019_get_epigenomic_peaks
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- NOTT2019_get_interactome
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- NOTT2019_get_promoter_interactome_data
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- NOTT2019_get_regulatory_regions
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- NOTT2019_plac_seq_plot
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- get_NOTT2019_superenhancer_interactome
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- title: CORCES2020 data
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desc: Single-cell epigenomic data from Corces et al. 2020
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contents:
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- CORCES2020_get_ATAC_peak_overlap
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- CORCES2020_get_hichip_fithichip_overlap
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- get_CORCES2020_bulkATACseq_peaks
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- get_CORCES2020_cicero_coaccessibility
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- get_CORCES2020_hichip_fithichip_loop_calls
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- get_CORCES2020_scATACseq_celltype_peaks
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- get_CORCES2020_scATACseq_peaks
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- title: GOSHIFTER
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desc: GoShifter enrichment analysis
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contents:
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- GOSHIFTER
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- GOSHIFTER_run
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- GOSHIFTER_heatmap
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- GOSHIFTER_histograms_SNPgroups
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- GOSHIFTER_histograms_pvals
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- title: MOTIFBREAKR
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desc: Motif disruption analysis
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contents:
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- MOTIFBREAKR
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- MOTIFBREAKR_calc_pvals
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- MOTIFBREAKR_filter
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- MOTIFBREAKR_plot
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- MOTIFBREAKR_summarize
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- title: XGR
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desc: Genomic region annotation via XGR
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contents:
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- XGR_enrichment
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- XGR_filter_assays
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- XGR_filter_sources
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- XGR_query
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- title: ROADMAP
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desc: Roadmap Epigenomics chromatin state annotations
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contents:
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- ROADMAP_construct_reference
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- ROADMAP_query
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- title: Plotting
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desc: Summary and visualization functions
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contents:
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- CS_bin_plot
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- CS_counts_plot
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- super_summary_plot
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- peak_overlap_plot
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- plot_dataset_overlap
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- plot_missense
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- convert_plots
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- merge_celltype_specific_epigenomics
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- title: Utilities
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desc: Helper functions
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contents:
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- add_mb
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- granges_overlap
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- get_window_limits
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- import_ucsc_bigwigs
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- test_enrichment

‎vignettes/cell_type_specific_epigenomics.Rmd‎

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---
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title: "Cell-type-specific epigenomics"
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author: "<h4>Author: <i>Brian M. Schilder</i></h4>"
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title: "Cell-type-specific epigenomics"
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author: "<h4>Author: <i>Brian M. Schilder</i></h4>"
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date: "<h4>Updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
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output:
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BiocStyle::html_document
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vignette: >
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%\VignetteIndexEntry{echoplot}
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%\VignetteIndexEntry{cell_type_specific_epigenomics}
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%\usepackage[utf8]{inputenc}
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%\VignetteEngine{knitr::rmarkdown}
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---
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```{r setup, echo=FALSE, include=FALSE}
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pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]
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library(pkg, character.only = TRUE)
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has_internet <- tryCatch(
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!is.null(curl::nslookup("github.com", error = FALSE)),
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error = function(e) FALSE
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)
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```
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```R
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## Nott2019
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`echoannot` includes data generated by
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["Nott2019"](https://doi.org/10.1126/science.aay0793):
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["Nott2019"](https://doi.org/10.1126/science.aay0793):
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> Nott A, Holtman IR, Coufal NG, ... Glass CK. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science. 2019 Nov 29;366(6469):1134-1139. doi: 10.1126/science.aay0793. Epub 2019 Nov 14. PMID: 31727856; PMCID: PMC7028213.
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### Import data
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### Import data
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```R
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```{r nott2019_import, eval=has_internet}
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superenhancers <- echoannot::get_NOTT2019_superenhancer_interactome()
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enhancers_promoters <- echoannot::NOTT2019_get_promoter_interactome_data()
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peaks <- echoannot::NOTT2019_get_epigenomic_peaks()
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peaks <- echoannot::NOTT2019_get_epigenomic_peaks()
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```
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### Plot
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```{r, eval=FALSE}
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```{r nott2019_plot, eval=has_internet}
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dat <- echodata::BST1
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histo_out <- echoannot::NOTT2019_epigenomic_histograms(dat = dat)
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```
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In addition to the plot object,
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In addition to the plot object,
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tables of both raw read ranges and called peaks are included in the output list.
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```{r, eval=FALSE}
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```{r nott2019_tables, eval=has_internet}
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knitr::kable(head(histo_out$data$raw))
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knitr::kable(head(histo_out$data$peaks))
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```
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## Corces2020
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`echoannot` also includes data generated by
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["Corces2019"](https://doi.org/10.1038/s41588-020-00721-x):
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> Corces, M.R., Shcherbina, A., Kundu, S. et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases. Nat Genet 52, 1158–1168 (2020). https://doi.org/10.1038/s41588-020-00721-x
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> Corces, M.R., Shcherbina, A., Kundu, S. et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nat Genet 52, 1158-1168 (2020). https://doi.org/10.1038/s41588-020-00721-x
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### Import data
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### Import data
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```R
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```{r corces2020_import, eval=has_internet}
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bulkATACseq_peaks <- echoannot::get_CORCES2020_bulkATACseq_peaks()
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cicero_coaccessibility <- echoannot::get_CORCES2020_cicero_coaccessibility()
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hichip_fithichip_loop_calls <- echoannot::get_CORCES2020_hichip_fithichip_loop_calls()
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### Plot
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```R
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*Note:* This chunk is kept as `eval=FALSE` because it depends on
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the `dat` variable from a prior analysis and `ggbio::autoplot`.
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```{r corces2020_plot, eval=FALSE}
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peak_dat <- echoannot::granges_overlap(
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dat1 = dat,
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dat1 = dat,
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chrom_col.1 = "CHR",
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start_col.1 = "POS",
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dat2 = scATACseq_celltype_peaks,
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dat2 = scATACseq_celltype_peaks,
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chrom_col.2 = "hg38_Chromosome",
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start_col.2 = "hg38_Start",
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end_col.2 = "hg38_Stop")
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ggbio::autoplot(peak_dat,
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ggplot2::aes(y=ExcitatoryNeurons, color=Effect))
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ggbio::autoplot(peak_dat,
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ggplot2::aes(y=ExcitatoryNeurons, color=Effect))
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```
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# Session Info
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# Session Info
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<details>
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<details>
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```{r Session Info}
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utils::sessionInfo()
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```
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</details>
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</details>

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