Nothing
## ---- echo = FALSE-------------------------------------------------------
knitr::opts_chunk$set(collapse=TRUE,comment="#>")
## ------------------------------------------------------------------------
library(LinkageMapView)
data(carrot)
head(carrot)
## ------------------------------------------------------------------------
library(qtl)
data(hyper)
class(hyper)
summary(hyper)
## ------------------------------------------------------------------------
outfile = file.path(tempdir(), "hyper.pdf")
lmv.linkage.plot(hyper,outfile,mapthese=c(1,4,6,15))
## ---- out.width = "680px",echo=FALSE-------------------------------------
knitr::include_graphics("hyper.png")
## ------------------------------------------------------------------------
outfile = file.path(tempdir(), "hyper_dupnbr.pdf")
lmv.linkage.plot(hyper,outfile,mapthese=c(1,4,6,15),dupnbr = TRUE)
## ---- out.width = "680px",echo=FALSE-------------------------------------
knitr::include_graphics("hyper_dupnbr.png")
## ------------------------------------------------------------------------
outfile = file.path(tempdir(), "hyper_showonly.pdf")
lmv.linkage.plot(hyper,outfile,mapthese=c(1,4,6,15),lcol="green",lcex=2,lfont=2,
rcol="red",rcex=2,rfont=3,
showonly=c("D1Mit123","D4Mit80","D6Mit135","D15Mit156"))
## ---- out.width = "680px",echo=FALSE-------------------------------------
knitr::include_graphics("hyper_showonly.png")
## ------------------------------------------------------------------------
outfile = file.path(tempdir(), "hyper_titles.pdf")
lmv.linkage.plot(hyper,outfile,mapthese=c(1,4,6,15),col.lgtitle = "blue",cex.lgtitle=2,
col.main = "red",main="Overall Title for the Output Map")
## ---- out.width = "680px",echo=FALSE-------------------------------------
knitr::include_graphics("hyper_titles.png")
## ------------------------------------------------------------------------
## plot a carrot comparative linkage map
## kindly provided by Massimo Iorizzo:
## Cavagnaro et al. BMC Genomics 2014, 15:1118
data(carrot)
# make a df to pass qtl info
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"
))
# make a list to pass label options
flist <- list()
locus <- c("BSSR-094", "K0149", "K0627", "K2161", "ESSR-087", "ESSR-057")
font <- c(2) #bold
flist[[1]] <- list(locus = locus, font = font)
locus <- c("F3H", "FLS1")
font <- c(4) #bold italic
flist[[2]] <- list(locus = locus, font = font)
locus <- c("P3", "P1", "Raa1")
font <- c(3) #italic
col <- c("red")
flist[[3]] <- list(locus = locus, font = font, col = col)
outfile = file.path(tempdir(), "carrot.pdf")
lmv.linkage.plot(
carrot,
outfile = 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
)
## ---- out.width = "500px",echo=FALSE-------------------------------------
knitr::include_graphics("carrot.png")
## ------------------------------------------------------------------------
## do a density map with default colors and customize the axis
data(oat)
## draw tickmarks at each cM from 0 to largest position of linkage groups to be drawn
maxpos <- floor(max(oat$Position[oat$Group == "Mrg01" | oat$Group == "Mrg02"]))
at.axis <- seq(0, maxpos)
## put labels on ruler at every 10 cM
axlab <- vector()
for (lab in 0:maxpos) {
if (!lab %% 10) {
axlab <- c(axlab, lab)
}
else {
axlab <- c(axlab, NA)
}
}
outfile = file.path(tempdir(), "oat_denmap.pdf")
lmv.linkage.plot(oat,outfile,mapthese=c("Mrg01","Mrg02"),denmap=TRUE, cex.axis = 1, at.axis = at.axis, labels.axis = axlab)
## ---- out.width = "120px",echo=FALSE-------------------------------------
knitr::include_graphics("oat_denmap.png")
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