An image plot visualization tool
Create a visualization of the models and variables selected by the iterative BMA algorithm.
An object of type 'bicreg', 'bic.glm' or 'bic.surv'
The color of the plot. The value "default" uses the current default R color scheme for image. The value "blackandwhite" produces a black and white image.
Other parameters to be passed to the image and axis functions.
This function is a modification of the
function from the
BMA package. The difference is that
variables (genes) with
probne0 equal to 0 are removed
before plotting. The arguments of this function is identical
to those in
An heatmap-style image, with the BMA selected variables on the vertical
axis, and the BMA selected models on the horizontal axis. The variables
(genes) are sorted in descreasing order of the posterior probability
that the variable is not equal to 0 (
probne0) from top to
bottom. The models are sorted in descreasing order of the
model posterior probability (
postprob) from left to right.
Biobase packages are required.
Clyde, M. (1999) Bayesian Model Averaging and Model Search Strategies (with discussion). In Bayesian Statistics 6. J.M. Bernardo, A.P. Dawid, J.O. Berger, and A.F.M. Smith eds. Oxford University Press, pages 157-185.
Yeung, K.Y., Bumgarner, R.E. and Raftery, A.E. (2005) Bayesian Model Averaging: Development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics 21: 2394-2402.
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library (Biobase) library (BMA) library (iterativeBMA) data(trainData) data(trainClass) ## training phase: select relevant genes ret.bic.glm <- iterateBMAglm.train (train.expr.set=trainData, trainClass, p=100) ## produce an image plot to visualize the selected genes and models imageplot.iterate.bma (ret.bic.glm)
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