vignettes/using_snp_plotter.md

Introduction

What is snp.plotter?

snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files.

What do snp.plotter images look like?

Here is a sample image as both a PDF and a EPS image. PDF images can be viewed using the free Adobe Reader software. EPS (or PDF) images can be viewed using front-end software for Ghostscript, a Postscript and PDF interpreter: Ghostview and GV for Unix/X11 systems and GSView for Windows.

snp.plotter example image

Who are the intended users of snp.plotter?

Researchers conducting gene association studies who need to create images showing results in the form of p-values of their work along with a linkage disequilibrium plot to show the underlying structure of the study population. Because snp.plotter is a visualization tool, the type of study design used either family-based, case-control, or a combination is irrelevant.

What are the main features of snp.plotter?

Usage

How do I install snp.plotter?

snp.plotter requires the installation of R, the statistical computing software, freely available here for Linux, Windows, or MacOS. snp.plotter uses three contributed packages: grid, lattice, and genetics available from the R Project website. snp.plotter can be downloaded CRAN. Packages in the current working directory of R can be installed using the install.packages command.

In Windows, make sure that you have downloaded the .zip version of a package, which is a pre-compiled binary. Change the word PACKAGE_FILENAME to the name of the package being installed.

install.packages("PACKAGE_FILENAME.zip", repos=NULL)

In Unix/Linux, make sure that you have downloaded a source package, the .tar.gz version, of a package. Change the word PACKAGE_FILENAME to the name of the package being installed.

install.packages("PACKAGE_FILENAME.tar.gz", repos=NULL)

The following error indicates that additional packages need to be installed: PACKAGE_FILENAME can be grid or genetics. These packages can be downloaded from CRAN. and installed using the same process described above.

Error: package 'PACKAGE_FILENAME' could not be loaded

How is snp.plotter used?

Once snp.plotter and its dependencies are installed, snp.plotter can be loaded into R using this command:

library(snp.plotter)

snp.plotter is then run using the following command. Explanation of snp.plotter configuration files and input files is provided in the file formats section. The configuration file specifies all the characteristics for the plot to be produced and the names of the data files to be used as input. Example configuration and input files are also provided.

snp.plotter(config.file = "config.txt")

Information about the configuration options is provided in the documentation on CRAN, which can viewed from within R using this command.

?snp.plotter

How do I incorporate the snp.plotter figures into my publication?

The listing below shows the most common scenarios for inclusion of a figure into a publication; methods will vary based on the intended publication type:

\documentclass{article}
\usepackage{graphicx}
\begin{document}
\begin{figure}
\includegraphics{FILENAME}
\end{figure}
\end{document}
gs -q -dNOPAUSE -dSAFER -dBATCH -r300 -g1050x1050 -sOutputFile=FILENAME.jpg -sDEVICE=jpeg FILENAME.eps

File Formats

What file types are used by snp.plotter?

snp.plotter uses tab-delimited text files as input files. These files can be created in a basic text editor such as Notepad in Windows or Excel saved as tab-delimited files using the "Save As" option. A dataset is composed a configuration file, a SNP and haplotype file for each result set, one genotype file, and an optional palette file. More information about these files can be found in the documentation on CRAN.

SNP.FILE=snp8_ss.txt,snp8_ss2.txt
HAP.FILE=snp8_haplo.txt,snp8_haplo2.txt
PALETTE.FILE=palette.txt
EVEN.SPACED=TRUE
USE.GBL.PVAL=TRUE
DISP.HAP=TRUE
DISP.LDMAP=FALSE
LD.COLOR.SCHEME=heat
COLOR.LIST=blue,red
SYMBOLS=circle,NA
PVAL.THRESHOLD=1
LAB.Y=ln
GENOTYPE.FILE=snp8_geno.txt
LD.TYPE=rsquare
DISP.COLOR.BAR=TRUE
DISP.TYPE=symbol
DISP.LEGEND=TRUE
SAMPLE.LABELS=Sample 1,Sample 2
IMAGE.TYPE=eps
DISP.SNP=TRUE
IMAGE.TITLE="8 SNP Example"
IMAGE.NAME=snp8_example
IMAGE.SIZE=3.5
ASSOC   SNP.NAME    LOC SS.PVAL
+   rs10_8  126272509   0.065
-   rs11_8  126274467   0.029
+   rs12_8  126275017   0.046
-   rs13_8  126275750   0.005
+   rs14_8  126283659   0.258
+   rs15_8  126284467   0.036
-   rs16_8  126298007   0.05
-   rs17_8  126299520   0.202
ASSOC   G.PVAL  I.PVAL  rs10_8  rs11_8  rs12_8  rs13_8  rs14_8  rs15_8  rs16_8  rs17_8
-   0.015   0.004   1   1   1                   
+   0.015   0.062   1   2   2                   
+   0.075   0.079       1   1   1               
+   0.075   0.039       2   2   2               
-   0.032   0.121           1   1   1           
+   0.032   0.153           1   2   2           
+   0.425   0.474               1   1   1       
+   0.425   0.003               2   2   2       
+   0.1 0.077                   1   1   1   
+   0.1 0.1                 1   2   2   
-   0.003   0.341                       1   1   1
+   0.003   0.001                       2   2   2
1   1   0   0   1   1   1   1   1   1
2   1   0   0   2   1   1   1   1   1
3   1   0   0   1   1   1   1   1   2
4   1   0   0   2   1   1   1   2   2
5   1   0   0   1   1   0   0   1   1
FFFFFF
CCCCFF
9999FF
6666FF
3333FF
0000FF
0000CC
000099
000066

Download

Where can I get the the source code of snp.plotter for my own project?

Author and Citation Information

Authors

Acknowledgements

Anushka Aqil for her feedback

Citation

Please cite the following publication, if you include figures generated with snp.plotter

Luna A, Nicodemus KK. snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package. Bioinformatics. 2007 Mar 15;23(6):774-6.



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snp.plotter documentation built on May 2, 2019, 9:31 a.m.