plot_genes: Plot boxplots and dotplots for genes and variables of...

In BIGslu/BIGpicture: Standard Plots for BIGslu

Plot boxplots and dotplots for genes and variables of interest

Description

Plot boxplots and dotplots for genes and variables of interest

Usage

plot_genes(
  dat = NULL,
  counts = NULL,
  meta = NULL,
  genes = NULL,
  fdr = NULL,
  libraryID = "libID",
  geneID = "ensembl_gene_id",
  subset_genes = NULL,
  variables,
  colorID = NULL,
  processors = NULL,
  subset.genes = NULL
)

Arguments

dat	DGEList or EList object with expression data (counts, E), sample metadata (samples, targets), and gene annotation (genes)
counts	If dat not provided. Data frame of gene expression. Genes are rows, samples are columns. geneID must be rownames or first column
meta	If dat not provided. Data frame of sample meta data with samples as rows.
genes	Optional if dat not provided. Data frame of gene annotation with genes as rows.
fdr	Optional. Model results output by kmFit( ). Used to label significant differences
libraryID	Character string of variable name to use when combining expression and sample data
geneID	Character string of variable name to use when combining expression and gene data
subset_genes	Optional. Character vector of genes to plot. Must match names in geneID column. If not provided, all genes are plotted.
variables	Character vector of variable names to include in plot. Variables can be character, factor, or numeric. One two-variable interaction term allowed
colorID	Optional. Character string for variable to color point by
processors	Numeric processors to run in parallel. Default is 2 less than the total available
subset.genes	Deprecated form of subset_genes

Value

List of ggplot objects

Examples

#Data from kimma
example.voom <- kimma::example.voom

subset_genes <- c("ENSG00000250479","ENSG00000250510","ENSG00000255823")

plot_genes(dat = example.voom, fdr = example.model$lmerel,
     subset_genes = subset_genes, geneID="geneName",
     variables = c("virus*asthma", "lib.size"), colorID = "virus")

BIGslu/BIGpicture documentation built on Oct. 14, 2024, 9:30 p.m.