ExploreModelMatrix is a small R package that lets the user interactively
explore a design matrix as generated by the model.matrix() R function.
In particular, given a table with sample information
and a design formula, ExploreModelMatrix illustrates the fitted values
from a general linear model (or, more generally, the value of the linear
predictor of a generalized linear model) for each combination of
input variables, simplifying understanding and generation of contrasts. A
number of other visualizations are also included in the interactive interface,
particularly simplifying the interpretation of linear models.
You can install ExploreModelMatrix from Bioconductor (note that you need
at least release 3.11 of Bioconductor, released in April 2020):
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ExploreModelMatrix")
The main function in the ExploreModelMatrix package is called
ExploreModelMatrix(). When calling ExploreModelMatrix(), simply provide a
data.frame (or DataFrame) with sample information and a design formula:
sampleData <- data.frame(genotype = rep(c("A", "B"), each = 4),
treatment = rep(c("ctrl", "trt"), 4))
ExploreModelMatrix(sampleData = sampleData,
designFormula = ~ genotype + treatment)
This will open up an R/Shiny application where you can explore the specified design matrix and the fitted values for each combination of predictor values.
For more examples of designs, we refer to the package vignette.