In uhlitz/dallianceR: A grammar of genome browsing with dalliance

knitr::opts_knit$set(root.dir = "../")

library(knitr)
library(dplyr)
library(dallianceR)

Quickstart

dallianceR is an interactive genome browser for R. It's based on JavaScript library dalliance and implemented in R with htmlwidgets. You can start by typing

dalliance()

It will open a blank genome browser with default reference genome GRCh38 and default annotation GENCODEv21 and is synonymous with:

dalliance(data = NULL, genome = "GRCh38", annotation = "GENCODEv21")

Predefined reference genomes and annotation data

Instead of default parameters, you can choose from a list of predefined reference genomes and annotation data:

ann_tab %>% 
  rename(Annotation = name) %>% 
  left_join(ref_tab %>% rename(reference = name), by = "reference") %>% 
  select(speciesName, reference, Annotation) %>% 
  setNames(c("Species", "Genome", "Annotation")) %>% 
  kable

Alternatively, you can define your own reference and annotation tracks and provide it as a list to dalliance:

my_annotation <- list(name = "GENCODEv19", 
                      desc = "Gene structures from GENCODE 21", 
                      bwgURI = "http://www.biodalliance.org/datasets/GRCh38/gencode.v21.annotation.bb",
                      stylesheet_uri = "http://www.biodalliance.org/datasets/GRCh38/gencode.v21.annotation.ix",
                      trixURI = "http://www.biodalliance.org/datasets/GRCh38/gencode.v21.annotation.ix")

my_genome <- list(speciesName = 'Human', 
                  taxon = '9606', 
                  auth = 'GRCh', 
                  version = '38', 
                  name = 'GRCh38', 
                  twoBitURI = 'http://www.biodalliance.org/datasets/hg38.2bit', 
                  desc = 'Human reference genome build GRCh38', 
                  tier_type = 'sequence', 
                  provides_entrypoints = 'true', 
                  pinned = 'true')

dalliance(genome = my_genome, annotation = my_annotation)

Add tracks to the browser

You can add tracks from files or GRanges objects:

• quantitative data: .bigbed, .bigwig or indexed .bam.
• or qualitative data: eg. .gff and .vcf (future)

Add tracks from bigwig files

If not organised in a GRanges objects, files (e.g. bigwig) need to be provided in a dataframe structure that specifies Experiment, Sample and Replicate and Path like this:

source("R/data.R")
dummy %>% kable

Say your dataframe is named my_data, you can call dalliance like this:

dalliance(data = my_data, genome = "GRCh38", annotation = "GENCODEv21")

Tracks belonging to the same Experiment are y-scaled together. By default replicates are overlayed in a single track. You can display them in individual tracks by setting combine_replicates = F:

dalliance(data = my_data, genome = "GRCh38", annotation = "GENCODEv21", combine_replicates = F)

Add GRanges list

TODO

uhlitz/dallianceR documentation built on May 3, 2019, 2:22 p.m.