Package: locusviz 0.3.0

locusviz: Yet Another Locus Visualization Package in R

This package provides various functions to visualize GWAS data for a locus of interest using ggplot2.

Authors:Masahiro Kanai

locusviz_0.3.0.tar.gz
locusviz_0.3.0.zip(r-4.7-any)locusviz_0.3.0.zip(r-4.6-any)locusviz_0.3.0.zip(r-4.5-any)
locusviz_0.3.0.tgz(r-4.6-any)locusviz_0.3.0.tgz(r-4.5-any)
locusviz_0.3.0.tar.gz(r-4.7-any)locusviz_0.3.0.tar.gz(r-4.6-any)
locusviz_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
locusviz/json (API)

# Install 'locusviz' in R:
install.packages('locusviz', repos = c('https://mkanai.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mkanai/locusviz/issues

Datasets:

On CRAN:

Conda:

3.35 score 3 stars 4 scripts 49 exports 150 dependencies

Last updated from:50c57c8211. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE495
source / vignettesOK341
linux-release-x86_64NOTE509
macos-release-arm64NOTE345
macos-oldrel-arm64NOTE384
windows-develNOTE490
windows-releaseNOTE399
windows-oldrelNOTE482
wasm-releaseOK242

Exports:annotate_hrangeannotate_r2binom_ciboot_cicompute_distance_to_genecompute_functional_enrichmentdistinct_shadesgencode_txdbgeom_jitter_textGeomJitterTextget_chromosome_sizesget_cs_color_mappingget_default_themeget_global_positionget_gnomad_colorsget_pfam_domainsget_tss_gene_bodyhighlight_vlinejitter_labelsliftover_variantload_txdbmean_cimedian_cina_andna_ornormalize_rankor_elseor_missingparse_variantplot_fm_panelplot_gene_panelplot_gene_score_panelplot_locuszoomplot_lollipopplot_manhattan_panelplot_r2_panelplot_upsetplot_upset_barplot_upset_matrixpreprocessscale_color_chromosomescale_x_chromosomespearman_cistat_summary_irqtrans_loglog_pUpSet2variant_strvariant_str2write_txdb_files

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encbeeswarmBHbinomBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbiovizBasebitbit64bitopsblobbootBSgenomebslibBuenColorscachemCairocheckmatecigarillocliclustercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdplyrensembldbepitoolsevaluatefarverfastmapfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbeeswarmggbioggplot2ggrastrgluegraphgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslOrganismDbipatchworkpillarpkgconfigplyrpngProtGenericspurrrR6raggrappdirsRBGLRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshadessnowSparseArraystringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviporviridisLitewithrxfunXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Annotate horizontal range on a plotannotate_hrange
Annotate variants with linkage disequilibrium (r2) valuesannotate_r2
Binomial confidence intervalbinom_ci
Bootstrap confidence intervalboot_ci
Compute distance from reference position to genescompute_distance_to_gene
Compute functional enrichment of variants by PIP binscompute_functional_enrichment
Generate distinct shades of a base colordistinct_shades
Create a TxDb object from GENCODE annotationsgencode_txdb
Text labels jittered to avoid horizontal overlapGeomJitterText geom_jitter_text
Get chromosome sizes and cumulative positionsget_chromosome_sizes
Get color mapping for credible setsget_cs_color_mapping
Get default ggplot2 theme for locusviz plotsget_default_theme
Convert chromosomal position to global genomic positionget_global_position
Get gnomAD population colorsget_gnomad_colors
Get Pfam domain annotations for a geneget_pfam_domains
Extract TSS and gene body information from TxDbget_tss_gene_body
Add vertical highlight lines to a plothighlight_vline
Jitter labels to avoid horizontal overlapjitter_labels
Liftover variant positions between genome buildsliftover_variant
Load transcript database for gene annotationsload_txdb
Mean confidence interval via bootstrapmean_ci
Median confidence interval via bootstrapmedian_ci
NA-safe AND operationna_and
NA-safe OR operationna_or
Normalize scores by rank with exponential decaynormalize_rank
Return first non-NA valueor_else
Conditionally return value or NULLor_missing
Parse variant string into componentsparse_variant
Create fine-mapping panelplot_fm_panel
Create gene track panelplot_gene_panel
Create gene score visualization panelplot_gene_score_panel
Create LocusZoom-style visualizationplot_locuszoom
Create lollipop plot for variant effectsplot_lollipop
Create Manhattan plot panelplot_manhattan_panel
Create r² (linkage disequilibrium) panelplot_r2_panel
Create UpSet plot for set intersectionsplot_upset
Plot UpSet bar panelplot_upset_bar
Plot UpSet matrix panelplot_upset_matrix
Preprocess GWAS data for visualizationpreprocess
Create chromosome color scale for Manhattan plotsscale_color_chromosome
Create chromosome x-axis scale for genome-wide plotsscale_x_chromosome
Spearman correlation confidence intervalspearman_ci
Summary statistic with interquartile rangestat_summary_irq
Create log-log transformation for p-valuestrans_loglog_p
TSS and gene body data for GENCODE v19 (hg19/GRCh37)tss_v19_hg19
TSS and gene body data for GENCODE v34 (hg38/GRCh38)tss_v34_hg38
TSS and gene body data for GENCODE v39 (hg38/GRCh38)tss_v39_hg38
Modified UpSet plotUpSet2
Create variant string from componentsvariant_str
Create variant string from locus and allelesvariant_str2
Write TxDb and TSS data fileswrite_txdb_files