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).

Usage

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

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.