Plot heatmap of merged gene expression data. — plotExpressionHeatmap • metapredict

Make a heatmap of gene expression from multiple datasets.

plotExpressionHeatmap(
  fitResult,
  lambda,
  ematMerged,
  sampleMetadata,
  annoLevels,
  annoColors = NA,
  clusterTogether = FALSE,
  geneIdOrder = NA,
  className = "class",
  classLevels = NA,
  org = "org.Hs.eg",
  maxVal = 3,
  ...
)

Arguments

fitResult	`glmnet` object.
lambda	value of lambda to use in `fitResult`.
ematMerged	matrix of gene expression for genes by samples.
sampleMetadata	data.frame of sample metadata.
annoLevels	Named list used to make the `annotation` argument passed to `pheatmap::pheatmap()`. Each name must correspond to a column name in `sampleMetadata`, and each item in the list must be a vector of values found in that particular column.
annoColors	Passed to `annotation_colors` argument of `pheatmap::pheatmap()`.
clusterTogether	logical indicating whether to cluster the samples from each dataset together or separately.
geneIdOrder	Optional character array of Entrez Gene IDs specifying the order of genes. If `NA` (default), the order from `makeCoefDt()` is used.
className	column in sampleMetadata containing values of the response variable.
classLevels	Order of classes for the column annotations.
org	Name of package for mapping Entrez Gene IDs to gene symbols, passed to `data` argument of `annotate::lookUp()`.
maxVal	Maximum absolute value of scaled and centered gene expression, used to control dynamic range of color in the heatmap.
...	Additional arguments passed to `pheatmap::pheatmap()`.

Value

A pheatmap object.