nplplot.old: LOD score plotting (old version of nplplot)

In nplplot: Plotting Linkage and Association Results

LOD score plotting (old version of nplplot)

Description

Plots score curves contained within one or more specified results files.

Usage

nplplot.old(files, col=2, row=2, mode="p", output="screen", 
          yline=2.0, ymin=NULL, ymax=NULL, yfix=FALSE, batch=FALSE, 
          headerfiles=NULL, titles=NULL, xlabl="", ylabl="", 
          lgnd="page", lgndx=NULL, lgndy=NULL, bw=TRUE, na.rm=TRUE)

Arguments

files	List of files names (strings). Each file produces a separate plot.
col	For multiple plots on a single page of pdf or postscript output, this item defines the number of columns of plots, and should be an integer greater than or equal to 1. Default is set to 2.
row	For multiple plots on a page of pdf or postscript output, this defines the number of rows of plots, (value should be 1 or greater). Default value is set to 2.
mode	Orientation for pdf or postscript output, "p" for portrait "l" for landscape.
output	File name for saving plots; "screen", the default causes the plots to be displayed on the screen. To produce a pdf file use the extension .pdf. To produce a postscript file, use the .ps file name extension. If no extension is given a pdf file is produced.
yline	Y-value for displaying a horizontal cut-off line.
ymin, ymax	Y-axis minimum and maximum values with default values NULL. If non-NULL values are provided, and yfix is set to TRUE, then the plot area will be cropped to these values.
yfix	Set to TRUE or FALSE depending on whether ymin and ymax should be enforced across all plots irrespective of whether the plot data lie within these bounds. Ignored if ymin or ymax are set to NULL.
batch	TRUE or FALSE, to determine whether the display screen should be closed. If nplplot is called within R, this should be set to FALSE.
headerfiles	List of file names, one for each data file specified above. Each header-file contains a string with column names corresponding to the columns in the data file. These column names are used in the plot legend. If set to NULL (the default), nplplot uses the first item in each column of a data file as plot legend. If a headerfile is provided, then nplplot will attempt to read in the first line of the datafile as data, so the user should be careful not to put in a headerline as well as a headerfile.
titles	Array of strings denoting titles for each plot. If there are not enough titles, the last string is recycled for the remaining plots. Default is an empty string.
xlabl	Array of strings, to use as the x-axis label on each plot.
ylabl	Array of strings to use as the y-axis label on each plot.
lgnd	TRUE, FALSE, "page" or a list of plot numbers denoting whether the legend should be drawn in all plots, none, first plot on a page, or specific plot numbers. Default "page".
lgndx	NULL or a real value if a specific x-coordinate should be used to position the legend. Default NULL.
lgndy	NULL or a real value if a specific y-coordinate should be used to position the legend. Default NULL.
bw	TRUE or FALSE depending on whether plots should be drawn in color. A list of six colors are defined within nplplot, which are successively used to draw each curve, and reused as necessary. The order in which these colors are used is: magenta, lightblue, grey, navyblue, lightcyan and pink. The 7th color, reserved for black and white plots is black.
na.rm	TRUE or FALSE depending on whether NAs should be removed prior to plotting the data. Including NAs will produce broken plots, when lines are drawn. This may be desirable in some cases, if missing data needs to be reported.

Details

Usually these results would be LOD scores, p-values, or log10(p-values). This is targetted towards p-values or LOD scores obtained at various marker positions from statistical analysis of genetic data. A results file has to be in a specific tabular format with each column separated by white-space :

A) First line = header line

B) Next set of lines = any number of data lines

C) Final two lines = line type & point type definition.

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  0.342                    
ltype    -99.99              1       2      3       
ptype    -99.99             15      16     17                  

In this example, line 1 column headers for the score columns may be used as labels within the legend, as described in the usage of the "headerfile" argument. The first two headers are ignored.

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.

The last two lines give line types and point types for each curve. A zero line or point type will not plot lines or points for that score column respectively. For allowable ptype values, consult the R documentation for "points". For line types, consult the documentation on "par".

The names in the first column are used as axis labels on the top of the plot border. Setting a name in the marker column to "-" will result in no label at that position.

Value

TRUE or FALSE depending on whether the input files were read in successfully.

See Also

nplplot, nplplot.multi

Examples

## Not run: nplplot.old("lod.1", output="lod.1.ps", batch=T, headerfiles="hdr.1")
## Not run: nplplot.old(c("lod.1", "lod.2"), col=1, row=2, headerfiles=c("hdr.1","hdr.2"))

nplplot documentation built on May 20, 2022, 1:07 a.m.