plot.OpenStatsFE: plot for an 'OpenStatsFE' object

In mpi2/OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

plot for an 'OpenStatsFE' object

Description

This function visualises an 'OpenStatsFE' object

Usage

 ## S3 method for class 'OpenStatsFE'
plot(x, main = "Mosaic plot", ask = FALSE, mfrow = c(2, 2), ...)

Arguments

x	an instance of ‘OpenStatsFE' result from OpenStatsAnalysis(method = ’FE') function
main	a string to be pasted to the title of the plots
ask	see 'ask' in 'par()' function. Default FALSE
mfrow	the screen partition. see 'mfrow' argument in the 'par' function. Default c(2,2) then all plots display in one screen.
...	other parameters that can be passed to the 'plot' function

Details

The plot function creates some visualisations for the Fisher's exact test framework:

- Mosaic plot of the response versus Genotype/Sex/LifeStage (if they exist in the data
- Mosaic plot of the Sex versus Genotype (if they exist in the data)

Value

Not applicable

Author(s)

Hamed Haseli Mashhadi <[e-mail]>

See Also

OpenStatsAnalysis, plot.OpenStatsRR, plot.OpenStatsMM

Examples

####################################################################
# Data preparation
####################################################################
#################
# Categorical data - Creating OpenStatsList object
#################
fileCat <- system.file("extdata", "test_categorical.csv", package = "OpenStats")
test_Cat <- OpenStatsList(
  dataset = read.csv(fileCat, na.strings = "-"),
  testGenotype = "Aff3/Aff3",
  refGenotype = "+/+",
  dataset.colname.genotype = "Genotype",
  dataset.colname.batch = "Assay.Date",
  dataset.colname.lifestage = NULL,
  dataset.colname.weight = "Weight",
  dataset.colname.sex = "Sex"
)
#################
# Fisher's exact test framework
#################
FE_result <- OpenStatsAnalysis(
  OpenStatsList = test_Cat,
  method = "FE",
  FE_formula = Thoracic.Processes ~ Genotype + Sex
)
plot(FE_result, col = 1:2)

mpi2/OpenStats documentation built on Sept. 17, 2022, 3:58 p.m.