gene.plot: gene.plot

In SNPtools: Accessing, subsetting and plotting mouse SNPs.

Description

Given a genomic region, plot the genes in the interval.

Usage

  gene.plot(mgi, col = "black", ...)

Arguments

mgi	Data.frame with MGI gene locations as returned by get.mgi.features{get.mgi.features}.
col	Color vector that is the color to use to plot genes. May be a single color for all genes or a vector with colors for each gene.
...	Other arguments to be passed into plot.

Details

The spacing algorithm attempts to organize the genes in such a way that they do not collide. Currently, this works 90

Value

Data.frame with gene locations and symbols.

Author(s)

Daniel Gatti

See Also

get.mgi.features{get.mgi.features}

Examples

  ## Not run: 
  data(example.genes)
  g = gene.plot(mgi = example.genes)
  
## End(Not run)

Example output

Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools

SNPtools documentation built on May 29, 2017, 3:12 p.m.