Description Usage Arguments Value Author(s) Examples
Creates an edgeR dispersion plot for RNA-Seq QC purposes. Takes a counts matrix or DGEList for input. Dispersion is plotted against AveLogCPM. Optionally, you can plot Biological Coefficient of Variation instead (BCV is the sqrt of dispersion).
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x |
A Counts matrix or DGEList (required) |
designMatrix |
A design matrix created stats::model.matrix |
plotType |
One of "dispersion" or "BCV" (default = "dispersion") |
symbolSize |
(Default=1) |
symbolShape |
see http://www.cookbook-r.com/Graphs/Shapes_and_line_types/ (Default = 1) |
symbolColor |
Default = "darkblue" |
symbolFill |
Default = "darkblue" |
symbolAlpha |
Transparency for the points. Value from 0 to 1. Smaller indicate more transparency (Default = 0.3) |
linefitSize |
(Default = 1) |
linefitColor |
(Default = "yellow") |
lineFit |
(Default = NULL) Any type supported by geom_smooth (loess is recommended). Defaults to NULL because enabling this overloads my poor 32bit PC. |
rugColor |
(Default = NULL) Set to Null to disable rug plots. Note: printing plots with rug plots can be slow (several minutes on my meager 32bit pc). So I left this disabled by default. Assign a valid color to enable |
rugAlpha |
Transparency for the rug plots (Default = 0.02) |
... |
Extra parameters to pass to edgeR::estimateDisp |
a ggplot object
John Thompson, jrt@thompsonclan.org
1 2 | MyGgplot <- plotDisp (MyDGElist)
MyGgplot <- plotDisp (MyDGEobj)
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