MANHATTAN++ is software to generate a transposed manhattan heatmap, implemented in R.
You need to install the latest version of R The R package can be run on Windows and Linux, you must specify paths to the filenames you are using as input and output.
To install the software from the GIT repository:
install.packages("devtools")
library(devtools)
install_github("cgrace1978/manhplot", dependencies = T, force = T)
The following command will run the plot with default data in the package. The pdf (test.pdf) will be created in the current working directory in R (This can be viewed using the getwd() command):
library(manhplot)
infile<-system.file("extdata","cad.add.160614_manhformat.txt.gz",package = "manhplot")
configfile<-system.file("extdata","config.txt", package = "manhplot")
snpfile<-system.file("extdata","56cad.add.160614.variants.txt", package = "manhplot")
## Run manhattan++ with the default paramaters and files included in the package
manhplusplot(infile = infile,outfile = "test", configfile = configfile, snpfile = snpfile)
For more information on using manhattan++ please visit the Manhattan++ wiki
To use Manhattan++ please cite the following paper:
Grace et al
Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers
BMC Bioinformatics 2019; 20(1):610
PubMed: 31775616