An R package to create a pretty Copy Number Variant plot from a segments file
This is early development so let me know if anyone finds this, likes it, or wants changes let me know!
PlotCNV was written on R 3.6.1 and I've no idea if it works on older versions.
It'll load/install ggplot2 and magrittr
As we're on github you'll need "install_github" from devtools.
## If you don't already have devtools installed
BiocManager::install("devtools")
library(devtools)
install_github("findlaycopley/PlotCNV")This will give you access to the wonderful world of PlotCNV ver 0.1.
You can generate a series of segments for hg19 like this:
CNV <- generateTestData()This will generate a dataframe to use in the package. This can be used as a guide to formatting your own data for use in this package.
| chr | sampleID | start.pos | end.pos | calls |
|---|---|---|---|---|
| chr7 | Sample1 | 100998668 | 110396599 | Loss |
| chr16 | Sample2 | 43859840 | 80317946 | Gain |
| chr12 | Sample3 | 32271933 | 99088557 | CN-LOH |
| chr16 | Sample4 | 58412150 | 88854473 | CN-LOH |
You can then run the following steps to get the plot
## Makes sure all the columns are labelled in a way that the package understands
CNV <- prepareCNV(CNV, chr="chr", sampleID="sampleID", start.pos="start.pos", end.pos="end.pos", calls="calls")
## Orders the samples so they will plot in descending order of % variant bp
CNV <- orderCNV(CNV)
## Sets up the data values for the plot
CNV <- setPositionsCNV(CNV, genome="hg19")
## Prints out the plot
CNV <- plotCopynumber(CNV)
## You can access the plot object in the Plots slot like this:
CNV@Plot$plotHere is the plot generated by the example data (I set the seed for the test data generator so yours should look identical.
