R/data_frame.R
track_data_frame.Rd
Creates the necessary configuration string for an R data frame so that it can be viewed as a track in a JBrowse custom linear genome view.
track_data_frame(track_data, track_name, assembly)
the data frame with track data. Must have cols:
chrom
, start
, end
, name
. The column
additional
can optionally be include with more feature information.
If a score
column is present, it will be used and the track will
be rendered to display quantitative features.
the name to use for the track
the config string generated by assembly
a character vector of stringified track JSON configuration
assembly <- assembly("https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", bgzip = TRUE)
df <- data.frame(
chrom = c(1, 2),
start = c(123, 456),
end = c(789, 101112),
name = c('feature1', 'feature2')
)
track_data_frame(df, "my_features", assembly)
#> [1] "{ \"type\": \"FeatureTrack\", \"name\": \"my_features\", \"assemblyNames\": [\"hg19\"], \"trackId\": \"hg19_my_features\", \"adapter\": { \"type\": \"FromConfigAdapter\", \"features\": [{\"refName\": \"1\", \"start\": 123, \"end\": 789, \"uniqueId\": \"adbb4b07e579c61e22035582cc5b5a16\", \"name\": \"feature1\", \"type\": \"\", \"additional\": \"\" }, {\"refName\": \"2\", \"start\": 456, \"end\": 101112, \"uniqueId\": \"adbb4b07e579c61e22035582cc5b5a16\", \"name\": \"feature2\", \"type\": \"\", \"additional\": \"\" }] } }"