CMplot (version 2.0.1)

CMplot-package: Circle Manhattan Plot

Description

Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out Genome-wide association study P-value results in both traditional rectangular patterns and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals.

Usage

CMplot(Pmap, col = c("red", "black", "green", "blue", "orange"), pch = 19,
	  band = 1, cir.band = 1, H = 1, out = "b", cex = c(0.5, 1), r = 1, 
	  outward = TRUE, line = TRUE, amplify = TRUE, cir.chr = TRUE, chr.band = 1, 
	  chr.col = NULL, cir.labels = TRUE, amplify.col = c("red", "green"))

Arguments

Pmap

a dataframe, at least four columns. The first column is the name of SNP, the second column is the chromosome of SNP, the third column is the position of SNP, and the remaining columns are the P-value of each trait(Note:each trait a column)

col

a vector, the colour for each chromosome, the colours are not fixed, one, two, three or more colours can be used, if the length of the col is shorter than the length the chromosome, then colours will be applied circularly.the default: col=c("red", "black"

pch

a number, the type for the points, is the same with "pch" in

band

a number, the space between chromosomes, the default is 1(if the band is 0, then there would be no space between chromosome)

cir.band

a number, the space between circles, the default is 1

H

a number, the height for each circle, each circle a trait, the default is 1

out

a character, only "c" or "m" or "b" can be used. if plottype="c",only circle-Manhattan plot will be plotted; if plottype="m",only Manhattan plot will be plotted; if plottype="b",both circle-Manhattan and Manhattan plots will be plotted;

cex

a vector, the size for the points, is the same with "size" in , and the first number controls the size of points in circle plot(the default is 0.5), the second number controls the size of points in Manhattan plot(the default is 1)

r

a number, the radius for the circle(the inside radius), the default is 1

outward

logical, if outward=TRUE,then all points will be plotted from inside to outside.

line

logical, CMplot can add two significant lines: significant1=-log10(1/makers), significant2=-log10(0.01/makers). if siglines=T,then two linse will be added to the plot.the default: amplify=TRUE

amplify

logical, CMplot can amplify the significant points, if amplify=T, then the points greater than significant1 will be 1.5 times bigger than normal, the default: amplify=TRUE

cir.chr

logical, a boundary represents chromosome, the default is TRUE

chr.band

a number, the width for the boundary, if cir.chr=FALSE, then this parameter will be useless.

chr.col

a character, the colour for the boundary, only one colour is allowed, if chr.col=NULL, then the default colours are the same with the parameter "col".

cir.labels

logical, whether to add the name of chromosome to the circle plot("S" means sex chromosome), the default: cir.labels=TRUE

amplify.col

a vector, the color for the points greater than significant1, the first colour controls the points which greater than significant1 and smaller than significant2, the second colour controls the points which greater than significant2,the default: amplify.co

Details

ll{ Package: CMplot Type: Package Version: 2.0.1 Date: 2015-06-015 License: GPL(>=2) }

Examples

#plot rectangular Manhattan only one trait with 20000 makers:
data(pig60K)                        
CMplot(pig60K[1:20000,c(1:4)],out="m")
 
################################################################################
#plot circular Manhattan for all traits with all makers:                       #
################################################################################
#data(pig60K)                                                                  #         
#CMplot(pig60K,col=c("gray30","gray60"),r=0.5,out="c",outward=FALSE,line=FALSE)#
################################################################################