pedvizapi


christian fuchsberger1, mario falchi2, lukas forer1, peter pramstaller1

1Institute of Genetic Medicine, European Academy, Bolzano, Italy
2Twin Research & Genetic Epidemiology Unit, Kings College London, London

Description Comparison In use Tutorials DemoApp Rpedviz Help Forum Download christian.fuchsberger@eurac.edu

Rpedviz (Alpha Version)

System requirements
Java VM 5.0/1.5 or higher Get Java
(To check Java version, type "java -version")
For 2.5D Visualization: Java 3D v1.4.2 or higher and up-to-date graphic card drivers.
The R project (>= 2.0.0)
rJava
and
pedviz_0.15.zip (2d + 2.5d + Rpedviz) of for *NIX pedviz_0.1.tgz (2d + 2.5d + Rpedviz)

Step by step guide
  • Fullfill system requirements
  • 2d visualization

    library(rJava)
    # update classpath
    .jinit(classpath="c:/pedviz_0.1.jar")
    pedviz <- .jnew("pedviz/rpedviz/RPedviz2D")

    .jcall(pedviz, "V", "addQualitativeTrait", "qtrait", 0, 1, 0.5, 0)

    # update data-path
    pedigree <- as.vector(readLines("c:/tutorial_data_2.csv"))
    format <- pedigree[1]
    data <- .jarray(pedigree[2:length(pedigree)])
    hints <- .jarray(c("qtrait"))

    .jcall(pedviz, "V", "plot", format, data, hints)

    Download rpedviz_2d.r (please adjust the class- and file-path).
    Download tutorial_data_2.csv


  • 2.5d visualization (pre-alpha)


    library(rJava)
    # update classpath; pedviz 3d + java 3d jar's have to be included
    .jinit(classpath="c:/pedviz_j3d_0.1.jar;C:/j3dcore.jar;C:/j3dutils.jar;C:/vecmath.jar;")
    pedviz <- .jnew("pedviz/rpedviz/RPedviz3D")

    .jcall(pedviz, "V", "addQualitativeTrait", "qtrait", 0, 1, 0.5, 0)

    pedigree <- as.vector(readLines("c:/tutorial_data_2.csv"))
    format <- pedigree[1]
    data <- .jarray(pedigree[2:length(pedigree)])
    hints <- .jarray(c("qtrait"))

    .jcall(pedviz, "V", "plot", format, data, hints)


    Download rpedviz_3d.r (please adjust the class- and file-path).
    Download tutorial_data_2.csv