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.Rhistory
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autoconnadj = TRUE, cex.axis = par("cex.axis"),
cex.lgtitle = par("cex.main"), cex.main = par("cex.main"),
col.axis = par("col.axis"), col.lgtitle = par("col.main"),
col.main = par("col.main"), conndf = NULL, denmap = FALSE,
header = FALSE,qtldf =qtldf,units = "cM")
lmv.linkage.plot(cross, outfile="map_Final.pdf", denmap = FALSE,
header = FALSE,qtldf =qtldf,units = "cM")
lmv.linkage.plot(cross, outfile="map_Final.pdf", denmap = FALSE,
header = FALSE,qtldf =qtldf,units = "cM")
lmv.linkage.plot(cross, outfile="map_Final.pdf", denmap = TRUE,
header = FALSE,qtldf =qtldf,units = "cM")
outfile = file.path(tempdir(), "hyper.pdf")
lmv.linkage.plot(cross, outfile, denmap = TRUE,
header = FALSE,qtldf =qtldf,units = "cM")
BiocManager::install("piano")
install.packages("piano")
install.packages("Biocmanger")
install.packages("gsaq")
install.packages("GSAQ")
install.packages("BiocManager")
BiocManager::install("piano")
lmv.linkage.plot(cross, outfile, ruler = TRUE,
lgtitle = c("2170", "70349", "10117"),
maxnbrcolsfordups = 2,
markerformatlist = flist,
lg.col = "lightblue1",
pdf.height = 16,
pdf.width = 10,
revthese = c("70349LG3"),
qtldf=qtldf)
lmv.linkage.plot(cross, outfile, ruler = TRUE,mapthese=c("CaLG01","CaLG02","CaLG03","CaLG04","CaLG05","CaLG06","CaLG07","CaLG08"),denmap=TRUE, cex.axis = 1, at.axis = at.axis, labels.axis = axlab)
lmv.linkage.plot(cross, outfile, ruler = TRUE,mapthese=c("CaLG01","CaLG02","CaLG03","CaLG04","CaLG05","CaLG06","CaLG07","CaLG08"),denmap=TRUE, cex.axis = 1,labels.axis = axlab)
lmv.linkage.plot(cross, outfile, ruler = TRUE,mapthese=c("CaLG01","CaLG02","CaLG03","CaLG04","CaLG05","CaLG06","CaLG07","CaLG08"),denmap=TRUE, cex.axis = 1)
lmv.linkage.plot(cross, outfile)
lmv.linkage.plot(cross, outfile,pdf.height = 30,
pdf.width = 30)
lmv.linkage.plot(cross, outfile,pdf.height = 35,
pdf.width = 35)
?lmvdencolor
lmvdencolor(cross,wsize = 35,bias = 5)
lmvdencolor(cross,wsize = 50,bias = 5)
lmvdencolor(cross,wsize = 50,bias = 5, colorin = colorRampPalette(RColorBrewer::brewer.pal(8, "Spectral"))(25)))
lmvdencolor(cross,wsize = 50,bias = 5, colorin = colorRampPalette(RColorBrewer::brewer.pal(8, "Spectral"))(25))
sectcoldf <- lmvdencolor(cross)
lmv.linkage.plot(cross, outfile,pdf.height = 35,
pdf.width = 35, )
lmv.linkage.plot(cross, outfile,pdf.height = 35,
pdf.width = 35, SETCOLDF)
lmv.linkage.plot(cross, outfile,pdf.height = 35,
pdf.width = 35, lmvdencolor)
lmv.linkage.plot(cross, outfile, lmvdencolor)
lmv.linkage.plot(cross,outfile,mapthese=c(1,2,3,4,5,6,7,8))
lmv.linkage.plot(cross,outfile)
?lmvdencolor
lmvdencolor(cross, wsize = 40, bias = 5,
colorin = colorRampPalette(RColorBrewer::brewer.pal(8, "Spectral"))(25))
new_color<-lmvdencolor(cross, wsize = 40, bias = 5,
colorin = colorRampPalette(RColorBrewer::brewer.pal(8, "Spectral"))(25))
new_color<-lmvdencolor(cross, wsize = 20, bias = 5,
colorin = colorRampPalette(RColorBrewer::brewer.pal(8, "Spectral"))(25))
new_color<-lmvdencolor(cross, wsize = 100, bias = 5,
colorin = colorRampPalette(RColorBrewer::brewer.pal(8, "Spectral"))(25))
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE,setcoldf=new_color)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE,new_color)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, sectcoldf = new_color)
outfile
qtl_all
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, sectcoldf = new_color, qtldf = qtl_all)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, sectcoldf = new_color, qtldf = qtl_all)
outfile
lmv.linkage.plot(cross, outfile, mapthese = NULL, sectcoldf = new_color, qtldf = qtl_all)
lmv.linkage.plot(cross, outfile, mapthese = NULL, qtldf = qtl_all)
lmv.linkage.plot(cross, outfile, mapthese = NULL, sectcoldf = new_color, qtldf = qtl_all)
qtl_all
lmv.linkage.plot(cross, outfile, qtldf = qtl_all)
outfile
qtl_all<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl_all.csv", header=none)
qtl_all<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl_all.csv", header=FALSE)
lmv.linkage.plot(cross, outfile, qtldf = qtl_all)
qtl_all
lmv.linkage.plot(cross, outfile, mapthese = NULL, sectcoldf = new_color, qtldf = qtl_all, ruler = TRUE)
lmv.linkage.plot(cross, outfile, mapthese = NULL, sectcoldf = mqtl_All, qtldf = qtl_all, ruler = TRUE)
lmv.linkage.plot(cross, outfile, mapthese = NULL, sectcoldf = new_color, qtldf = qtl_all, ruler = TRUE)
mqtl_All
qtl_all
qtldf
lmv.linkage.plot(cross, outfile, mapthese = NULL, qtldf)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtl_all)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf,
data.frame(
chr = "70349LG3",
qtl = "RTPE-Q1",
so = 36.6,
si = 37,
ei = 37,
eo = 38,
col="red"
))
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2)
qtldf <- rbind(qtldf,
data.frame(
chr = "CaLG02",
qtl = "RTPE-Q1",
so = 36.6,
si = 37,
ei = 37,
eo = 38,
col="red"
))
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
QTLDF<-rbind(qtldf,qtl_all)
QTLDF
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2)
qtldf <- rbind(qtldf,
data.frame(
chr = "CaLG02",
qtl = "RTPE-Q1",
so = 36.6,
si = 37,
ei = 37,
eo = 38,
col="red"
))
qtldf
QTLDF
qtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl.csv", header=FALSE)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
qtldf
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2)
qtldf <- rbind(qtldf,
data.frame(
chr = "CaLG02",
qtl = "RTPE-Q1",
so = 36.6,
si = 37,
ei = 37,
eo = 38,
col="red"
))
qtldf
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf,
data.frame(
chr = "CaLG02",
qtl = "RTPE-Q1",
so = 36.6,
si = 37,
ei = 37,
eo = 38,
col="red"
))
qtldf
qtldf <- rbind(qtldf, qtl)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
qtldf <- rbind(qtldf, qtl)
qtldf
qtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl.csv")
qtldf <- rbind(qtldf, qtl)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
qtldf
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2)
mqtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\mqt_new.csv")
mqtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\mqtl_new.csv")
mqtl
sectcoldf<-mqtl
sectcoldf
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2, sectcoldf = sectcoldf)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2)
qtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl.csv")
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2)
?qtldf
qtldf<-qtldf()
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2, units = cM, ruler = TRUE)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2, sectcoldf = sectcoldf)
new_color
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2, sectcoldf = new_color)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2, sectcoldf = new_color,posonleft = TRUE)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2, sectcoldf = new_color, posonleft = TRUE)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2, sectcoldf = new_color, posonleft = TRUE)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 2, sectcoldf = new_color, posonleft = FALSE)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont = 13)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont = bold)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold')
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', lg.lwd='bold')
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', lg.lwd=3)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', lg.lwd=10)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', pdf.pointsize=13)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25)
?lmvdencolor
new_color<-lmvdencolor(cross, wsize = 200, bias = 2)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25)
new_color<-lmvdencolor(cross, wsize = 500, bias = 6)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25)
new_color<-lmvdencolor(cross, wsize = 50, bias = 6)
new_color<-lmvdencolor(cross, wsize = 100, bias = 6)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, maxnbrcolsfordups = 4, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=4)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=4)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=3)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=1)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, pdf.family = 'Arial')
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, pdf.family = 'Ariel')
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, pdf.family = 'Helvicta')
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, pdf.family = "Helvetica"
)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=3)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10)
?lmv.linkage.plot
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, posonleft=rep(FALSE,3))
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, posonleft=rep(FALSE,8))
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, posonleft=rep(FALSE,12))
qtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl.csv")
qtldf <- rbind(qtldf, qtl)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
qtldf
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, posonleft=rep(FALSE,12))
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10)
qtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl.csv")
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),
stringsAsFactors = FALSE
)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(), size = numeric(),shape=numeric()
stringsAsFactors = FALSE
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(), size = numeric(), shape = numeric()
stringsAsFactors = FALSE
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),cex = numeric(),
stringsAsFactors = FALSE
)
qtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl.csv")
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),cex = numeric(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, pdf.width = 13, pdf.height = 13)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, pdf.width = 50, pdf.height = 50)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, pdf.width = 60, pdf.height = 60)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, pdf.width = 60, pdf.height = 60, pdf.pointsize=15)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, pdf.width = 60, pdf.height = 60, pdf.family = "Bebas")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd.axis=10, pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd=10, pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtlscanone = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd=10, pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = (qtldf,lwd =5) sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd=10, pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = (qtldf,lwd =5), sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd=10, pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = (qtldf,cex =5), sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd=10, pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, lwd=10, pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8, cex=10, pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8,pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica")
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8,pdf.width = 60, pdf.height = 60, pdf.family = "Helvetica", rcex=10)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8,pdf.width = 60, pdf.height = 40, pdf.family = "Helvetica", rcex=10)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont = 'bold', pdf.pointsize=25, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),cex = numeric(),
stringsAsFactors = FALSE
)
qtldf
qtldf <- rbind(qtldf, qtl)
qtldf
qtldf
qtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl.csv")
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),cex = numeric(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
qtldf
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(),
col = character(),cex = character(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=25, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =10)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =5)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =3)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =2)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 65, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.7)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 70, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.5)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 80, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.5)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 80, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.5, qtlw=0.5)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(),
eo = numeric(), col()
stringsAsFactors = FALSE
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(), eo = numeric(), col = character(), pch = numeric(),
stringsAsFactors = FALSE
)
qtl<-read.csv("C:\\Users\\ishit\\OneDrive\\Documents\\Chickpea\\qtl.csv")
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(), eo = numeric(), col = character(), pch = numeric(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 80, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.5, qtlw=0.5)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 80, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.5)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, pch =15, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 80, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.5)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = (qtldf, pch =15), sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 80, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.5)
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 80, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.5)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(), eo = numeric(), col = character(), pch=15,
stringsAsFactors = FALSE
)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(), eo = numeric(), col = character(), pch=15,
stringsAsFactors = FALSE)
qtldf
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(), eo = numeric(), col = character(), pch = numeric(), pch=15, cex =15,
stringsAsFactors = FALSE
)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(), eo = numeric(), col = character(), pch = numeric(), pch=15,
stringsAsFactors = FALSE
)
qtldf <- data.frame(
chr = character(),
qtl = character(),
so = numeric(),
si = numeric(),
ei = numeric(), eo = numeric(), col = character(), pch = numeric(),
stringsAsFactors = FALSE
)
qtldf <- rbind(qtldf, qtl)
qtldf
lmv.linkage.plot(cross, outfile, mapthese = NULL, denmap = TRUE, qtldf = qtldf, sectcoldf = new_color, rfont ='bold', pdf.pointsize=30, lgperrow=8,pdf.width = 80, pdf.height = 40, pdf.family = "Helvetica", rcex=10, lgw =0.5)
library(ggplot2)
?ggplot2
library(dplyr)
library(tidyverse)
library(tidyverse)