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.
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 ONE7(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
>