Last data update: 2014.03.03

R: Method "categoricalBarplot"
categoricalBarplotR Documentation

Method "categoricalBarplot"

Description

Graph function for the Fisher Exact Test framework's results. Creates stacked bar plot(s) to compare proportions seen in a categorical variable between different genotypes. Graphs are created for all data and also for each sex individually.

Usage

    categoricalBarplot(phenTestResult,outputMessages=TRUE)

Arguments

phenTestResult

instance of the PhenTestResult class that comes from the function testDataset; mandatory argument

outputMessages

flag: "FALSE" value to suppress output messages; "TRUE" value to show output messages; default value TRUE

Author(s)

Natalja Kurbatova, Natasha Karp, Jeremy Mason

References

Karp N, Melvin D, Sanger Mouse Genetics Project, Mott R (2012): Robust and Sensitive Analysis of Mouse Knockout Phenotypes. PLoS ONE 7(12): e52410. doi:10.1371/journal.pone.0052410

West B, Welch K, Galecki A (2007): Linear Mixed Models: A practical guide using statistical software New York: Chapman & Hall/CRC 353 p.

See Also

PhenList

Examples

    file <- system.file("extdata", "test_categorical.csv", package="PhenStat")
    test <- PhenList(dataset=read.csv(file),
            testGenotype="Aff3/Aff3")
    result <- testDataset(test,
            depVariable="Thoracic.Processes",
            method="FE")       
    categoricalBarplot(result)
    

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PhenStat)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PhenStat/categoricalBarplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: categoricalBarplot
> ### Title: Method "categoricalBarplot"
> ### Aliases: categoricalBarplot
> 
> ### ** Examples
> 
>     file <- system.file("extdata", "test_categorical.csv", package="PhenStat")
>     test <- PhenList(dataset=read.csv(file),
+             testGenotype="Aff3/Aff3")
Warning:
Dataset's column 'Assay.Date' has been renamed to 'Batch' and will be used for the batch effect modelling.

Warning:
Dataset has been cleaned by filtering out records with genotype value other than test genotype 'Aff3/Aff3' or reference genotype '+/+'.

Warning:
Dataset's 'Weight' column is missed.
You can define 'dataset.colname.weight' argument to specify column for the weight effect modeling.

Information:
Dataset's 'Genotype' column has following values: '+/+', 'Aff3/Aff3'

Information:
Dataset's 'Sex' column has following value(s): 'Female', 'Male'

Warning:
Weight column is not present in the database.

>     result <- testDataset(test,
+             depVariable="Thoracic.Processes",
+             method="FE")       
Information:
Dependent variable: 'Thoracic.Processes'.

Information:
Method: Fisher Exact Test framework with filtered dataset.

>     categoricalBarplot(result)
>     
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>