lmv.linkage.plot {LinkageMapView}

LinkageMapView plotting function

Description

lmv.linkage.plot is the main function to produce linkage group maps and has many parameters to customize the pdf output.

Usage

lmv.linkage.plot(mapthis, outfile, mapthese = NULL, at.axis = NULL,
  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,
  dupnbr = FALSE, font.axis = par("font.axis"),
  font.lgtitle = par("font.main"), font.main = par("font.main"),
  header = TRUE, labdist = 0.3, labels.axis = TRUE, lcex = par("cex"),
  lcol = par("col"), lfont = par("font"), lgperrow = NULL,
  lgtitles = NULL, lgw = 0.25, lg.col = NULL, lg.lwd = par("lwd"),
  lty.axis = "solid", lwd.axis = 1, lwd.ticks.axis = lwd.axis,
  main = NULL, markerformatlist = NULL, maxnbrcolsfordups = 3,
  pdf.bg = "transparent", pdf.family = "Helvetica", pdf.fg = "black",
  pdf.width = NULL, pdf.height = NULL, pdf.pointsize = 12,
  pdf.title = "LinkageMapView R output", posonleft = NULL,
  prtlgtitles = TRUE, qtldf = NULL, revthese = NULL, rcex = par("cex"),
  rcol = par("col"), rfont = par("font"), roundpos = 1, rsegcol = TRUE,
  ruler = FALSE, sectcoldf = NULL, segcol = NULL, qtlscanone = NULL,
  showonly = NULL, units = "cM", ylab = units)

Arguments

mapthis

Required, either a 'cross' object from r/qtl, a csv or txt file or a data frame with the following 3 columns in this order:

1. Required, linkage group name. This will be the title for the linkage group unless overridden - see lgtitles.

2. Required, position - must be in numerical order ascending within linkage group name.

3. Required, locus - marker name at this position.

4. Optional, segcol - color for the line across the chromosome at this marker. See also segcol parameter.

outfile

Required, name for the output pdf file.

mapthese

Optional vector of linkage group names to print. The default, NULL, will print all linkage groups in mapthis.

at.axis

Optional. The points at which tick-marks are to be drawn on the ruler. Non-finite (infinite, NaN or NA) values are omitted. By default (when NULL) tickmark locations are computed. #' @seealso axis

autoconnadj

If TRUE (the default), locus with the same name (homologs) on adjacent linkage groups will be connected with a line.

cex.axis

The magnification to be used for axis (ruler) text. The default is par("cex.axis").

cex.lgtitle

The magnification to be used for linkage group titles. The default is par("cex.main").

cex.main

The magnification to be used for main title. The default is par("cex.main").

col.axis

The color to be used for axis (ruler) text. Defaults to par("col.axis").

col.lgtitle

The color to be used for linkage group titles. Defaults to par("col.main").

col.main

The color to be used for the main title. Defaults to par("col.main").

conndf

An optional data frame containing markers to be connected with lines (homologs). If autoconnadj = TRUE, these lines will appear as well as those with the same name in adjacent linkage groups. Required columns:

• fromchr Linkage group for the line start.

• fromlocus Locus name for the line start.

• tochr Linkage group for the line end.

• tolocus Locus name for the line end.

denmap

If TRUE, you are requesting a density map which means no locus or position labels will be printed and the following parameters are set: ruler = TRUE autoconndf = FALSE conndf = NULL See also sectcoldf parameter

dupnbr

If TRUE, only the first marker name at a position will print with (## more) afterwards indicating the number of duplicate markers at that position. dupnbr should be left to the default, FALSE, if showonly provided.

font.axis

An integer which specifies which font to use for the axis (ruler) text. The default is par("font.axis"). 1 is plain text. 2 is bold. 3 is italic. 4 is bold italic.

font.lgtitle

An integer which specifies which font to use for the linkage group titles text. The default is par("font.main"). 1 is plain text. 2 is bold. 3 is italic. 4 is bold italic.

font.main

An integer which specifies which font to use for title text. The default is par("font.main"). 1 is plain text. 2 is bold. 3 is italic. 4 is bold italic.

header

A boolean indicating if the input file has a header row. Default is TRUE.

labdist

Distance in inches from the chromosome to the position and locus labels. The default is 0.3 inches.

labels.axis

Optional. This can either be a logical value specifying whether (numerical) annotations are to be made at the tickmarks on the ruler, or a character or expression vector of labels to be placed at the tickpoints. If this is not logical, at should also be supplied and of the same length. The default is TRUE.

lcex

A numerical value giving the amount by which position labels should be magnified. The default is par("cex"). See also rcex for locus labels.

lcol

The color for the position labels. The default is par("col"). See also rcol for locus labels.

lfont

An integer which specifies which font to use for the position labels. The default is par("font"). See also rfont for locus labels.

lgperrow

An integer specifying how many linkage groups to plot in one row. As many rows as needed to plot all requested linkage groups will be plotted.

lgtitles

Optional vector of titles for the linkage groups. These will override the default, which is that the linkage group names in the input print as titles. This may be useful if in mapthese you have indicated to print the same linkage group more than once for the purpose of showing homologous markers without having lines cross. See also cex.lgtitle, col.lgtitle, font.lgtitle

lgw

Width of chromosome in inches. Default is 0.25 inches.

lg.col

Linkage group color. The color of the chromosomes. The default is the background color (pdf.bg).

lg.lwd

Linkage group linewidth. The width of the line around the chromosome. Defaults to par("lwd").

lty.axis

Optional. Line type for both the axis line and the tick marks.

lwd.axis

Optional. Line width for the axis line. The default is 1.

lwd.ticks.axis

Optional. Line width for the axis tick marks. Default is lwd.axis

main

An optional title for the linkage group map. See also cex.main, col.main, and font.main.

markerformatlist

An optional list containing the following vectors:

• locus Required. A vector of loci for which the following should be applied.

• col Optional. The color for these locus labels. This color will override rcol. See also rsegcol.

• cex Optional. A numerical vlue giving the amount by which these locus labels should be magnified. This value will override rcex.

• font Optional. An integer which specifies which font to use for these locus labels. This value will override rfont.

maxnbrcolsfordups

Indicates the number of columns across the page for locus labels appearing at duplicate positions. The default is 3.

pdf.bg

Background color for the pdf. Default is "transparent".

pdf.family

Font family for all text. Default is "Helvetica".

pdf.fg

Foreground color for the pdf. Default is black.

pdf.width

Width of the output file in inches. Defaults to the size necessary to fit all linkage groups with other options specified.

pdf.height

Height of the output file in inches. Defaults to the size necessary to fit all linkage groups with other options specified.

pdf.pointsize

The default point size to be used. Defaults to 12.

pdf.title

Title to be passed to pdf as metadata. This title does not appear except in the pdf metadata. Defaults to "LinkageMapView R output".

posonleft

A vector of boolean (TRUE or FALSE) the length of the number of linkage groups to be plotted. If FALSE, print positions on right hand side of linkage group and locus names on left hand side of linkage group. Default is TRUE.

prtlgtitles

If FALSE do not print linkage group titles. Default is TRUE.

qtldf

An optional data frame containing QTL information for plotting. The data frame, if provided, must contain:

• chr Linkage group name for QTL.

• qtl Name (label) for QTL.

• so Start of outer interval. Numeric.

• si Start of inner interval. Numeric.

• ei End of inner interval. Numeric.

• eo End of outer interval. Numeric.

• col Color for QTL.

revthese

Optional vector of linkage group names to reverse. The end position becomes position 0 and position 0 becomes the end position.

rcex

A numerical value giving the amount by which locus labels should be magnified. The default is par("cex"). See also lcex for position labels.

rcol

The color for the locus labels. The default is par("col"). See also lcol for position labels.

rfont

An integer which specifies which font to use for the locus labels. The default is par("font"). See also lfont for position labels.

roundpos

Number of positions after the decimal point to print for positions. Default is 1

rsegcol

Color of the segments across the chromosome and to the label. TRUE, the default, indicates the color should be the same as the label.

ruler

A single boolean (TRUE OR FALSE). If TRUE, an axis is drawn on the left hand side of the page and the position labels are not printed on any linkage group. The default is FALSE.

sectcoldf

Optional data frame containing the following named columns indicating sections of the chromosome to be colored:

• Required, chr - matches from input file or cross object linkage group name

• Required, s - start position in cM

• Required, e - end position in cM

• Required, col - color for section

• Optional, dens - a numeric cm / marker value used to print the density map legend.

For a density map, use the lmvdencolor function to populate sectcoldf. When denmap = TRUE and no sectcoldf parameter is supplied, lmvdencolor is called with defaults fully populating the sectcoldf data frame. See also the denmap parameter.

@seealso lmvdencolor

segcol

Optional. Name of the column in mapthis that contains colors for the line segments across the chromosome. If specified, this overrides rsegcol.

qtlscanone

Optional scanone data frame from package r/qtl. If provided, all QTLs in the dataframe will be drawn by calculating their start and end with the r/qtl function bayesint with defaults.

showonly

Optional vector of marker names. If provided, only these marker names will be printed.

units

Units of the position values supplied in mapthis. The default value is cM (centimorgan) but any value can be provided. The value provided is only used for a ruler (y axis) title and the density map legend text.

ylab

Optional. Title for the y-axis (ruler). The default value is units. See units parameter.

Examples

## take a cross object from r/qtl and produce linkage map
## on chr 1,4,6,15

library(qtl)
data(hyper)
outfile = file.path(tempdir(), "hyper.pdf")
lmv.linkage.plot(hyper,outfile,mapthese=c(1,4,6,15))

## color some of the markers for emphasis

library(qtl)
data(hyper)

# make a list to pass label options
flist <- list()
locus <- c("D1Mit123","D1Mit105","D6Mit273","D15Mit56","D15Mit156")
col   <- c("red")
flist[[1]] <- list(locus=locus,col=col)

outfile = file.path(tempdir(), "hyperred.pdf")
lmv.linkage.plot(hyper,outfile,mapthese=c(1,4,6,15),markerformatlist=flist)

## change some of the pdf options and chromosome color
## changing linkage group title color (col.lgtitle) to same as
## foreground pdf color

library(qtl)
data(hyper)

outfile = file.path(tempdir(), "hyperlg.pdf")
lmv.linkage.plot(hyper,outfile,
mapthese=c(1,4,6,15),
pdf.bg="black",pdf.fg="white",col.lgtitle="white",
pdf.height=8,pdf.title="myhyper",lg.col="tan")

## change all label colors and fonts

library(qtl)
data(hyper)

outfile = file.path(tempdir(), "hypercol.pdf")
lmv.linkage.plot(hyper,outfile,mapthese=c(1,4,6,15),
lcol="blue",lfont=2,lcex=1.2,rcol="red",rfont=3,rcex=2)

## make a dataframe to pass sections of chr to col
## use a ruler instead of printing positions as labels
## only allow one column for duplicate markers at same position
## (default is 3)

library(qtl)
data(hyper)

chr = c(1, 4, 6, 15)
s = c(82,35,9.8,7.7)
e = c(94,47,21.9,13.1)
col = c("pink","blue","blue","green")
sectcoldf <-  data.frame(chr, s, e, col,stringsAsFactors = FALSE)

outfile = file.path(tempdir(), "hyperruler.pdf")
lmv.linkage.plot(hyper,outfile,mapthese=c(1,4,6,15),
ruler=TRUE,maxnbrcolsfordups = 1, sectcoldf=sectcoldf)

## plot qtls also out of a r/qtl scanone object
## plot marker names on left (instead of right) of chr 4 and 7

library(qtl)
data(hyper)

# create scanone df for testing
hyper <-
 calc.genoprob(hyper,
               step = 2.0,
               map.function = "haldane",
               stepwidth = "fixed")
hyper.scanone <- scanone(hyper)

outfile = file.path(tempdir(), "testrqtlhyper2.pdf")
lmv.linkage.plot(hyper,
   outfile, mapthese=c(1,4,6,7,15),
   qtlscanone = hyper.scanone,
   posonleft = c(TRUE,FALSE,TRUE,FALSE,TRUE))

## Not run: 
## plot a carrot comparative linkage map
## kindly provided by Massimo Iorizzo:
## Cavagnaro et al. BMC Genomics 2014, 15:1118

# 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)
filename <- system.file("extdata", "Carrot.csv", package="LinkageMapView")
outfile = file.path(tempdir(), "carrot.pdf")
lmv.linkage.plot(
  mapthis = filename,
  outfile = outfile,
  ruler = TRUE,
  lgtitle = c("2170", "70349", "10117"),
  maxnbrcolsfordups = 1,
  markerformatlist = flist,
  lg.col = "lightblue1",
  pdf.width =10,
  revthese = c("70349LG3"),
  qtldf=qtldf
)

## End(Not run)

## do a density map with default colors
data(oat)

outfile = file.path(tempdir(), "oat_Mrg01.pdf")
lmv.linkage.plot(oat,outfile,mapthese=c("Mrg01","Mrg02"),denmap=TRUE)

## Not run: 
## do a density map and provide your own colors with lmvdencolor helper
data(oat)
##
outfile = file.path(tempdir(), "oat_Mrg01_YlGn.pdf")

sectcoldf <- lmvdencolor(oat,colorin =
colorRampPalette(RColorBrewer::brewer.pal(8, "YlGn"))(5))

lmv.linkage.plot(oat,outfile,denmap=TRUE,sectcoldf=sectcoldf)

## End(Not run)