Description Usage Arguments Details Value Note Author(s)
View source: R/HLP_genelabels_plot.R
Plotting of genes and exones incl. gene labels
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | regionalplot.genelabels(
genes,
levels,
exons,
xstart,
xstop,
ystart,
ygenesize,
scale.factor,
arrow.scale.factor = scale.factor,
truncate = TRUE,
genecol = "forestgreen",
genenamecol = "black"
)
|
genes |
a dataframe of genes to plot, with columns |
levels |
integer giving desired number of layers to plot multiple genes. Genes are assigned to
layers via gene start position. If NULL, an additional column |
exons |
a data frame containing columns |
xstart |
an integer number defining the smallest base position of the plot packet. |
xstop |
an integer number defining the largest base position of the plot packet. |
ystart |
numeric y position of the line marking the gene. |
ygenesize |
numeric y extentsion. |
scale.factor |
character expansion value as in e.g |
arrow.scale.factor |
character expansion value for arrows. |
truncate |
When TRUE, gene start / end positions will be truncated to xstart and xstop. Exons with exon_chrom_start > xstop or exon_chrom_end < xstart are dicarded (that are those that lie completely beyond xstart and xstop). |
genecol |
character giving gene color. |
genenamecol |
character giving color of gene names. |
Shows an arrow (orientation = strand) and the according gene symbol in the plot. Can also mark exons with a thickening of the gene line.
no value returned. Genes are plotted in active graphics device.
Arrowheads are omitted (with a warning) on any arrow of length less than 1/1000 inch
(see help(arrows)
from graphics package)
Milan Hiersche and Frank Ruehle
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