nplplot {nplplot}

Plotting statistics along a chromosome

Description

Plots linkage or association statistics along a chromosome, contained within a data frame or a file. Marker names are displayed along the top border.

Usage

nplplot(plotdata=NULL, filename=NULL, yline=2.0, ymin=0, ymax=3.0,
         header=TRUE, yfix=FALSE, title=NULL, draw.lgnd=TRUE,
         xlabl="", ylabl="", lgndx=NULL, lgndy=NULL, lgndtxt=NULL,
         cex.legend = 0.7, cex.axis=0.7, tcl=1,
         bw=TRUE, my.colors=NULL, ltypes=NULL, ptypes=NULL,
         na.rm=TRUE, plot.width=0.0, ...) 

Arguments

plotdata

A data frame containing marker names in the first column, marker map positions in the second column, and statistical scores in column 3 onwards.

filename

A table format file containing the plot data as described above.

header

TRUE or FALSE depending on whether the plotdata or file has a header line.

yline

Y-value for displaying a horizontal cut-off line. If 'yfix' is set to TRUE and Y-line falls outside of [ymin, ymax], then the cut-off line is omitted.

ymin, ymax

Y-axis minimum and maximum values. If non-NULL values are provided, and yfix is set to TRUE, then the plot area will be cropped to these values. If yfix is set to FALSE, then ymin and ymax values are ignored.

yfix

TRUE or FALSE to denote whether plot area should be cropped to the ymin, ymax values. This has no effect if ymin, ymax values are NULL.

title

Used as the subtitle of the plot.

xlabl

X-axis label. May interfere with the display of the subtitle provided as the title argument.

ylabl

Y-axis label.

draw.lgnd

TRUE or FALSE denoting whether a plot legend should be displayed.

lgndx

X coordinate for the legend box, passed to the legend command. Ignored if draw.legend is set to FALSE. If set to NULL with draw.legend set to TRUE, the X-coordinate is automatically calculated.

lgndy

Y coordinate for the legend box, passed to the legend command. Ignored if draw.legend is set to FALSE. If set to NULL with draw.legend set to TRUE, the Y-coordinate is automatically calculated.

lgndtxt

Vector of strings to use in the legend.

cex.legend

Character scaling for legend, passed as the cex argument to the legend command.

cex.axis

Character scaling for the axis, passed to the axis command for drawing the top border.

tcl

Length of ticks for the top border, passed to the axis command.

bw

TRUE or FALSE depending on whether plots should be drawn in color. If set to FALSE, then the colors defined by my.colors are used.

my.colors

Vector of color specifications as described in the par command. Ignored if bw above is set to FALSE. If bw is to TRUE and my.colors is set to NULL, the rainbow palette will be used.

ltypes

Vector of line types for the plots. Each non-zero line type is passed on to a lines command. Use 0 or 'none' if a line is to be skipped. If NULL, no lines will be drawn. For line types see the par command. If set to "default", line-types 1 through the number of plots is used.

ptypes

Vector of characters giving the point types, to be passed onto the points command. Use 'none' if no points are to be drawn for a score column. If NULL, no points will be displayed. If both the line-type and point-type specification for a results column is set to 'none', that column will not be plotted.

na.rm

TRUE or FALSE depending on whether points with Y-coordinates set to NAs should be skipped. Setting na.rm to TRUE eliminates discontinuities in the plots.

plot.width

A number giving the width of the plot in inches. This is used to decide whether some marker names should be dynamically hidden, if they are too close to each other along the top border. If set to 0, the default page-size is used to set the width.

...

Further graphical parameters to be passed onto the 'plot', 'lines' and 'points' commands.

Details

The nplplot function draws multiple curves within a single plot by automatically calling 'plot', 'lines', and 'points' multiple times, thus making it easy for the user to plot many columns of results using a single plot command. It is intended for the display of linkage and association analysis results such as LOD scores and P-values. It allows the marker names to be displayed along the top border of the plot, as well as a significance threshold line.

The input plot data has to be in a specific tabular format with each column separated by white-space :

Here is an example:

Marker   Position        score1  score2 score3      
d1s228   0.00            0.546   0.345  0.142                    
d1s429   1.00            0.346   0.335  0.252       
d1s347   2.00            0.446   0.245  0.342                    

This example file contains a header, therefore the header argument should be set to TRUE.

Lines 2-4 contain scores at various marker positions. Missing scores can be denoted with either "." or "NA". The position column cannot have missing data. There can be any number of score columns within a file and will be plotted as separate curves within the same plot. Each file is plotted as a separate plot.

Value

TRUE or FALSE depending on whether the plot data was successfully plotted.

See Also

nplplot.multi, nplplot.old

Examples

# plot with legend
par(omi=c(0.05, 0.05, 0.5, 0.05))
data(lods1, package="nplplot")
nplplot(plotdata=lods1, draw.lgnd=TRUE)

# plot without legend
data(lods2, package="nplplot")
nplplot(plotdata=lods2, draw.lgnd=FALSE)

# plotting from a data file
datadir <- paste(system.file("data", package="nplplot"), .Platform$file.sep, sep="")
nplplot(filename=paste(datadir, "lods2.txt.gz", sep=""))