nplplot {nplplot} | R Documentation |
Plots linkage or association statistics along a chromosome, contained within a data frame or a file. Marker names are displayed along the top border.
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, ...)
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 y-fix 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,
an 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,
an 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. |
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.
A results file has to be in a specific tabular format with each column separated by white-space :
Here is an example:
marker location 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 0.342This 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.
TRUE or FALSE depending on whether the plot data was successfully plotted.
# 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", sep=""))