Plot bar plots for gene abundance or fold change

This function generates bar plots for gene abundance or fold change, normalized by either a reference gene or centered to the mean. The user can also plot the contrast of two conditions.

Usage

rna.plot_bar(
  dds,
  genes,
  type = c("contrast", "centered"),
  shrunken.lfc = T,
  contrast = NULL,
  col.id = "ID",
  name_table = NULL,
  match.id = "Accession",
  match.name = "Name",
  convert_name = FALSE,
  shape.size = 2.5,
  collage = TRUE,
  plot = TRUE,
  export = TRUE,
  export.nm = NULL
)

Arguments

dds: A DESeqDataSet object containing the data.
genes: A vector of gene names or IDs.
type: Type of plot: "centered" or "contrast".
shrunken.lfc: A logical indicating if shrunken log2 fold changes should be used if type = "contrast". Default is TRUE.
contrast: Name of the contrast for plotting when type is "contrast".
col.id: Name of the column with gene IDs in dep.
name_table: A data frame containing the mapping of gene names to reference names.
match.id: The name of a column in name_table to find matches with col.id.
match.name: The name of a column in name_table to assign new names based on matches of col.id and match.id.
convert_name: Logical value indicating whether to convert the gene names to reference names based on name_table (e.g., gene names).
shape.size: Numeric value defining the (replicate) symbol size in the plot
collage: A logical indicating if multiple plots for different genes should be combined into collages of up to 8 plots. Default is TRUE.
plot: wether to return the plot or not.
export: Logical; whether to export the plot as PDF an PNG files
export.nm: Name of the output PDF and PNG files if export = TRUE.

Value

If plot is set to FALSE and the length of genes is less than or equal to 8, a data frame with the log2 fold changes or log2 intensities, along with their lower and upper bounds of 95% confidence intervals, is returned.