plotGenes: plots gene structure or transcript structures
In Sushi: Tools for visualizing genomics data

plots gene structure or transcript structures

plotGenes(geneinfo = NULL, chrom = NULL, chromstart = NULL,
  chromend = NULL, col = SushiColors(2)(2)[1], bheight = 0.3,
  lheight = 0.3, bentline = TRUE, packrow = TRUE, maxrows = 10000,
  colorby = NULL, colorbyrange = NULL,
  colorbycol = colorRampPalette(c("blue", "red")), types = "exon",
  plotgenetype = "box", arrowlength = 0.005, wigglefactor = 0.05,
  labeltext = TRUE, labeloffset = 0.4, fontsize = 0.7, fonttype = 2,
  labelat = "middle", ...)

`geneinfo`	gene info stored in a bed-like format. If NULL it will look up genes in the region using biomart (with biomart="ensembl" and dataset="hsapiens_gene_ensembl"). See also `useMart`
`chrom`	chromosome of region to be plotted
`chromstart`	start position
`chromend`	end position
`col`	single value or vector specifying colors of gene structures
`bheight`	the height of the boxes drawn for exons
`lheight`	the height of the bent line is bent is set to TRUE
`bentline`	TRUE/FALSE indicating whether lines between exons should be bent
`packrow`	TRUE / FALSE indicating whether genes should be packed or whether each gene should be plotted on its own row
`maxrows`	The maximum number of rows to plot on the y-axis
`colorby`	vector to scale colors by
`colorbyrange`	the range of values to apply the color scale to. Values outside that range will be set to the limits of the range.
`colorbycol`	palette to apply color scale to (only valid when colorby is not NULL)
`types`	single value or vector specifying types of elements (acceptable values are 'exon','utr')
`plotgenetype`	String specifying whether the genes should resemble a 'box' or a 'arrow'
`arrowlength`	value (between 0 and 1) specifying the length of the tail of each arrow as a fraction of the total plot width (only valid when plotgenetype is set to "arrow")
`wigglefactor`	the fraction of the plot to leave blank on either side of each element to avoid overcrowding.
`labeltext`	TRUE/FALSE indicating whether genes should be labeled
`labeloffset`	value (between 0 and 1) specifying the vertical offset of gene labels
`fontsize`	font size of gene labels
`fonttype`	font type of gene labels
`labelat`	postion along gene to place labels (acceptable values are "middle","start",and "end")
`...`	values to be passed to `plot`

data(Sushi_genes.bed)

chrom            = "chr15"
chromstart       = 72998000
chromend         = 73020000
chrom_biomart    = 15

plotGenes(Sushi_genes.bed,chrom_biomart,chromstart,chromend ,types=Sushi_genes.bed$type,
     maxrows=1,height=0.5,plotgenetype="arrow",bentline=FALSE,col="blue",
     labeloffset=1,fontsize=1.2)

labelgenome( chrom, chromstart,chromend,side=1,scipen=20,n=3,scale="Mb",line=.18,chromline=.5,scaleline=0.5)

Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: biomaRt
[[1]]
NULL

[[2]]
function (n) 
{
    x <- ramp(seq.int(0, 1, length.out = n))
    if (ncol(x) == 4L) 
        rgb(x[, 1L], x[, 2L], x[, 3L], x[, 4L], maxColorValue = 255)
    else rgb(x[, 1L], x[, 2L], x[, 3L], maxColorValue = 255)
}
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