PlotGeneSet {myTAI} | R Documentation |
Plot the Expression Profiles of a Gene Set
Description
This function simply visualizes the gene expression profiles of
a defined subset of genes stored in the input ExpressionSet
.
Usage
PlotGeneSet(
ExpressionSet,
gene.set,
get.subset = FALSE,
use.only.map = FALSE,
colors = NULL,
plot.legend = TRUE,
y.ticks = 6,
digits.ylab = 4,
...
)
Arguments
ExpressionSet |
a standard PhyloExpressionSet or DivergenceExpressionSet object. |
gene.set |
a character vector storing the gene ids for which gene expression profiles shall be visualized. |
get.subset |
a logical value indicating whether or not an |
use.only.map |
a logical value indicating whether instead of a standard |
colors |
colors for gene expression profiles. Default: |
plot.legend |
a logical value indicating whether gene ids should be printed as legend next to the plot. |
y.ticks |
a numeric value specifying the number of ticks to be drawn on the y-axis. |
digits.ylab |
a numeric value specifying the number of digits shown for the expression levels on the y-axis. |
... |
additional parameters passed to |
Details
This function simply visualizes or subsets the gene expression levels of a set of genes
that are stored in the input ExpressionSet
.
Author(s)
Hajk-Georg Drost
See Also
SelectGeneSet
, PlotEnrichment
, DiffGenes
Examples
data(PhyloExpressionSetExample)
# the best parameter setting to visualize this plot:
# png("test_png.png",700,400)
PlotGeneSet(ExpressionSet = PhyloExpressionSetExample,
gene.set = PhyloExpressionSetExample[1:5, 2],
type = "l",
lty = 1,
lwd = 4,
xlab = "Ontogeny",
ylab = "Expression Level")
# dev.off()
# In case you would like to work with the expression levels
# of selected genes you can specify the 'get.subset' argument:
PlotGeneSet(ExpressionSet = PhyloExpressionSetExample,
gene.set = PhyloExpressionSetExample[1:5, 2],
get.subset = TRUE)
# get a gene subset using only a phylostratihraphic map
ExamplePSMap <- PhyloExpressionSetExample[ , 1:2]
PlotGeneSet(ExpressionSet = ExamplePSMap,
gene.set = PhyloExpressionSetExample[1:5, 2],
get.subset = TRUE,
use.only.map = TRUE)