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Detailed Descriptions
 

BioIDE contains many innovative data visualization tools that will surely help researchers undertand their data better. Once you have BioIDE installed, you will immediately see the benefits those tools bring to you. Not to bore our visitors with a long list of data visualization widgets, below we provide some in-depth description on a few.

PedigreeView

PedigreeView is a next-generation pedigree drawing program that will automatically draw large and complex pedigree structures for multi-generation families. As long as family IDs, individual IDs, and parent IDs are specified in the original data file, after the data is loaded into BioIDE, PedigreeView will draw a family tree for each family. A researcher can either glide through all families using a slider controller or select a few to be displayed on the same graph.

PedigreeView enjoys several advanced features:

  • Able to handle consanguinous loops within an extended family
  • Able to handle multiple mating individuals
  • Able to handle multiple founding groups
  • Allow easy configuration of the pedigree tree such as node size, node distance, font size, font style, etc.
  • Allow easy export as image of drawn pedigree tree for publication

One extremely useful feature in PedigreeView that is lacking in most pedigree drawing software is the ability to allow a user to specify the phenotypes and markers to be displayed for each individual in the pedigree tree. For example, if result from a data analysis suggests that the presence of a particular combination of genotypes for two markers is closely associated with the clinical endpoint, then the user can choose the clinical endppoint from a drop-down list of available phenotypes, choose those two markers from a list of available markers, and PedigreeView will display the phenotype and genotype values for those three variables for each individual in a family tree.


PatternGraph

PatternGraph is an network-drawing component in BioIDE. Although currently it is only used in conjuction with Pattern Examiner to display the relationship among markers in patterns, it can accommodate a huge variaty of graphs. As an interactive graph, PatternGraph gives users the freedom to scale or rotate the graph, move graph nodes around, choose to display names for verteces or edges, choose to display weight for edges, filtering on edge weight so that only a subset of vertexes and edges are shown, etc.


PhenotypeProfileView

As its name suggests, PhenotypeProfileView displays the frequency of values for each phenotype in a dataset in a bar graph. Beyond that, PhenotypeProfileView offers several cool features. For example, a slider allows a user to slide through all phenotypes one by one. A user can also select a few phenotypes to see their profiles at the same time. Most of the customization allowed by Microsoft Excel are enabled. For example, the graph can be zoomed, saved, printed, etc. One can change the title, the font, and the axis labels.


PhenotypeScatterView

PhenotypeScatterView is another way to look at phenotype data than PhenotypeProfileView. A scatter plot will be built after a user specifies the phenotypes to be used for the X axis and the Y axis. The user can specify more than one plot to show all plots at the same time. Missing values often cause trouble on these kind of plots but PhenotypeScatterView allows a user to specify the desired method to deal with missing data.


HardyWeinbergQQPlot

HardyWeinbergQQPlot draws a line graph using P values obtained from Hardy-Weinberg Equilibrium test. A reference line indicating the null hypothesis is also drawn. Any data points that deviate from the null hypothesis are worth further investigation.


MissingDataView

MissingDataView is a simple line graph to show the percentage of missing data in a dataset. Because a genotyping dataset usually contain marker genotypes on individuals, the percentage of missing genotype data can be organized according to markers or individuals. As a result, options are provided in MissingDataView so that a user can choose to display marker-based missing data percentages or individual-based missing data percentages.


HaploView

Haploview is designed to simplify and expedite the process of haplotype analysis and was developed by the Mark Daly lab at the Borad Institute. It is an excellent program for LD & haplotype block analysis, haplotype population frequency estimation, single SNP and haplotype association tests, and permutation testing for association significance, among others. Please visit Haploview at MIT for details. Haploview is a java program and can be downloaded as a component of BioIDE.



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