| Type: | Package |
| Title: | The Manhattan++ Plot |
| Depends: | R (≥ 3.4.0) |
| Version: | 1.1 |
| Date: | 2019-11-25 |
| Author: | Chris Grace <cgrace@well.ox.ac.uk> |
| Maintainer: | Chris Grace <cgrace@well.ox.ac.uk> |
| Description: | This plot integrates annotation into a manhattan plot. The plot is implemented as a heatmap, which is binned using -log10(p-value) and chromosome position. Annotation currently supported is minor allele frequency and gene function high impact variants. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| RoxygenNote: | 6.1.1 |
| Imports: | reshape2, ggplot2, ggrepel, gridExtra |
| Suggests: | R.utils, testthat |
| URL: | https://github.com/cgrace1978/manhplot/ |
| BugReports: | https://github.com/cgrace1978/manhplot/issues |
| NeedsCompilation: | no |
| Packaged: | 2019-11-25 15:53:19 UTC; cgrace |
| Repository: | CRAN |
| Date/Publication: | 2019-11-25 16:40:03 UTC |
The Manhattan++ Plot
Description
This plot integrates annotation into a manhattan plot. The plot is implemented as a heatmap, which is binned using -log10(p-value) and chromosome position. Annotation currently supported is minor allele frequency and gene function high impact variants.
Details
The DESCRIPTION file:
| Package: | manhplot |
| Type: | Package |
| Title: | The Manhattan++ Plot |
| Depends: | R (>= 3.4.0) |
| Version: | 1.1 |
| Date: | 2019-11-25 |
| Author: | Chris Grace <cgrace@well.ox.ac.uk> |
| Maintainer: | Chris Grace <cgrace@well.ox.ac.uk> |
| Description: | This plot integrates annotation into a manhattan plot. The plot is implemented as a heatmap, which is binned using -log10(p-value) and chromosome position. Annotation currently supported is minor allele frequency and gene function high impact variants. |
| License: | GPL (>= 2) |
| RoxygenNote: | 6.1.1 |
| Imports: | reshape2, ggplot2, ggrepel, gridExtra |
| Suggests: | R.utils, testthat |
| URL: | https://github.com/cgrace1978/manhplot/ |
| BugReports: | https://github.com/cgrace1978/manhplot/issues |
| NeedsCompilation: | no |
| Packaged: | 2019-11-25 15:02:16 UTC; cgrace |
| Repository: | CRAN |
| Date/Publication: | 2019-06-04 11:40:03 UTC |
Index of help topics:
manhplot-package The Manhattan++ Plot manhplusplot Generate the manhattan++ plot
Author(s)
Chris Grace <cgrace@well.ox.ac.uk>
Maintainer: Chris Grace <cgrace@well.ox.ac.uk>
Generate the manhattan++ plot
Description
Generate the manhattan++ plot
Usage
manhplusplot(infile, outfile, configfile, snpfile, drawastiff = F,
GWS = 5e-08, FDR = 0.001, MAF = 0.05, chrname = "chr",
posname = "pos", pvalname = "pvalue", frqname = "maf",
conseqname = "conseq", showgenes = F, showrsids = F,
pos.split = 3e+06, pval.split = 0.125, max.pval = 20)
Arguments
infile |
Input GWAS summary statistics |
outfile |
Output file prefix for the manhattan++ plot |
configfile |
Configuration file |
snpfile |
Table of SNPs to visualize |
drawastiff |
If TRUE draw a Tiff file, if FALSE draw a PDF file |
GWS |
Genome wise significance pvalue threshold (5E-8 by default) |
FDR |
False discovery Rate pvalue threshold (1E-3 by default) |
MAF |
Minor Allele Frequency threshold |
chrname |
Column name for chromosome in GWAS infile |
posname |
Column name for position in GWAS infile |
pvalname |
Column name for pvalue in GWAS infile |
frqname |
column name for allele frequency in GWAS infile |
conseqname |
column name for variant annotation consequence in GWAS infile |
showgenes |
If T shows known genes as bubbles on main manhattan plot, if F show positions of interest as bubbles |
showrsids |
If showgenes is T, then show the rsids, rather than genes |
pos.split |
The bin lengths for positions |
pval.split |
The bin lengths for pvalues |
max.pval |
The maximum pvalue to display |
Details
For file formats see github page https://github.com/cgrace1978/manhplot
Author(s)
Chris Grace
Examples
library(manhplot)
## Load R.utils for gzip functionality
library(R.utils)
## unzip the data included with this package
gunzip(system.file("extdata","cad.add.160614_manhformat.txt.gz",package = "manhplot"))
infile<-system.file("extdata","cad.add.160614_manhformat.txt",package = "manhplot")
configfile<-system.file("extdata","config.txt", package = "manhplot")
snpfile<-system.file("extdata","56cad.add.160614.variants.txt", package = "manhplot")
manhplusplot(infile = infile,outfile = file.path(tempdir(), "default-plot"),
configfile = configfile, snpfile = snpfile)
## zip the data
gzip(system.file("extdata","cad.add.160614_manhformat.txt",package = "manhplot"))