MultiManhattan: Drawing multi-locus Manhattan plot

In mrMLM: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for GWAS

Drawing multi-locus Manhattan plot

Description

Using the results of the mrMLM software to draw a multi-locus Manhattan plot

Usage

MultiManhattan(ResultIntermediate,ResultFinal,mar=c(2.9,2.8,0.7,2.8), 
LabDistance=1.5,ScaleDistance=0.4,LabelSize=0.8,ScaleSize=0.7,
AxisLwd=5,TckLength=-0.03,LogTimes=2,LODTimes=1.2,lodline=3, 
dirplot=getwd(), PlotFormat="tiff", 
width=28000,height=7000,pointsize = 60,res=600,
MarkGene=FALSE,Pos_x=NULL,Pos_y=NULL,GeneName=NULL,
GeneNameColour=NULL,...)

Arguments

ResultIntermediate	Intermediate results obtained by the mrMLM software,"D:/Users/ResultIntermediate.csv".
ResultFinal	Final results obtained by the mrMLM software,"D:/Users/ResultFinal.csv".
mar	A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot, and the default is c(2.9, 2.8, 0.7, 2.8).
LabDistance	Distance between label and axis; the default is 1.5.
ScaleDistance	Distance between scale values and axis; the default is 0.4.
LabelSize	Size of all the three labels; the default is 0.8.
ScaleSize	Size of scale values; the default is 0.7.
AxisLwd	The width of axis, a positive number; the default is 5.
TckLength	The length of tick marks; the default is -0.03.
LogTimes	Magnification of -log10(P-value); the default is 2.
LODTimes	Magnification of LOD score; the default is 1.2.
lodline	The significant LOD score; the default is 3.
dirplot	Path to save plot; the default is current working directory
PlotFormat	Format of the plot.i.e., *.tiff, *.png, *.jpeg, *.pdf
width	Figure width; the default is 28000.
height	Figure height; the default is 7000.
pointsize	Word resolution, with the unit of 1/72 inch, being pixels per inch (ppi); the default is 60.
res	Figure resolution, with the unit of pixels per inch (ppi); the default is 600.
MarkGene	To mark genes in plot or not; if "TRUE" is selected, a file, namely "Reference information to mark gene.csv", that contains the x and y axis information of all the significant QTNs will generate. The default is "FALSE", indicating that no candidate or known gene names are marked in Manhattan plot.
Pos_x	Numeric vectors of x axis where the text labels should be written.
Pos_y	Numeric vectors of y axis where the text labels should be written.
GeneName	A character vector or expression specifying the text to be written.
GeneNameColour	The colour of gene names.
...	Arguments passed to points, axis, text.

Author(s)

Zhang Ya-Wen, Wang Jing-Tian, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[e-mail]>

Examples

inter<-data(ResultIntermediate)
fin<-data(ResultFinal)
MultiManhattan(ResultIntermediate=ResultIntermediate,ResultFinal=ResultFinal,dirplot=tempdir())

mrMLM documentation built on March 27, 2022, 9:05 a.m.