Using the results of the mrMLM software to draw a multi-locus Manhattan plot
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,...)Intermediate results obtained by the mrMLM software,"D:/Users/ResultIntermediate.csv".
Final results obtained by the mrMLM software,"D:/Users/ResultFinal.csv".
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).
Distance between label and axis; the default is 1.5.
Distance between scale values and axis; the default is 0.4.
Size of all the three labels; the default is 0.8.
Size of scale values; the default is 0.7.
The width of axis, a positive number; the default is 5.
The length of tick marks; the default is -0.03.
Magnification of -log10(P-value); the default is 2.
Magnification of LOD score; the default is 1.2.
The significant LOD score; the default is 3.
Path to save plot; the default is current working directory
Format of the plot.i.e., *.tiff, *.png, *.jpeg, *.pdf
Figure width; the default is 28000.
Figure height; the default is 7000.
Word resolution, with the unit of 1/72 inch, being pixels per inch (ppi); the default is 60.
Figure resolution, with the unit of pixels per inch (ppi); the default is 600.
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.
Numeric vectors of x axis where the text labels should be written.
Numeric vectors of y axis where the text labels should be written.
A character vector or expression specifying the text to be written.
The colour of gene names.
Arguments passed to points, axis, text.
# NOT RUN {
inter<-data(ResultIntermediate)
fin<-data(ResultFinal)
MultiManhattan(ResultIntermediate=ResultIntermediate,ResultFinal=ResultFinal,dirplot=tempdir())
# }
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