Plot coefficients for a gene expression meta-analysis.

Make a ggplot of the coefficients from a glmnet object trained on a gene expression meta-analysis (either logistic or multinomial classification).

plotCoefficients(
  fitResult,
  lambda,
  classLevels = NA,
  decreasing = FALSE,
  geneIdOrder = NA,
  org = "org.Hs.eg"
)

Arguments

fitResult	glmnet object.
lambda	value of lambda to use in `fitResult`.
classLevels	Order of classes in the confusion matrix. If `NA` (default), then the function uses the order in `fitResult`.
decreasing	logical indicating whether to sort genes by decreasing coefficient.
geneIdOrder	Optional character array of Entrez Gene IDs specifying the order of genes. If `NA` (default), the order from `makeCoefDt()` is used.
org	Name of package for mapping Entrez Gene IDs to gene symbols, passed to `data` argument of `annotate::lookUp()`.

A ggplot object.