Plot bar plots for protein abundance or fold change

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

Usage

prot.plot_bar(
  dep,
  proteins,
  combine = FALSE,
  type = c("contrast", "centered", "ReferenceProt", "ReferenceCondition", "abundance"),
  ref.prot = NULL,
  ref.condition = NULL,
  contrast = NULL,
  col.id = "ID",
  name_table = NULL,
  match.id = "Accession",
  match.name = "Name",
  convert_name = FALSE,
  shape.size = 2.5,
  y.lim = NULL,
  basesize = 12,
  plot = TRUE,
  export = FALSE,
  export.nm = NULL,
  width = NULL,
  height = NULL
)

Arguments

dep: A SummarizedExperiment object containing the data.
proteins: A vector of protein names or IDs.
combine: Logical value indicating whether to combine the data from different proteins in one plot.
type: Type of plot: "abundance", "ReferenceProt", "ReferenceCondition", "centered", or "contrast".
ref.prot: ID or name of the reference protein for normalization when type is "ReferenceProt".
ref.condition: Name of the reference condition by which all average abundance values are divided when type is "ReferenceCondition".
contrast: Name of the contrast for plotting when type is "contrast".
col.id: Name of the column with protein IDs in dep.
name_table: A data frame containing the mapping of protein 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 protein names to reference names based on name_table (e.g., gene names).
shape.size: Numeric value defining the (replicate) symbol size in the plot.
y.lim: Limits of the y axis (numeric vector of length 2). If NULL, will be inferred from data (unless combine=TRUE, then each chunk is plotted without that inference).
basesize: Base font size for the plot theme.
plot: Whether to immediately print/return the plot(s).
export: Logical; whether to export the plot(s) as PDF and PNG files.
export.nm: Name of the output PDF and PNG files if export = TRUE.
width: Numeric value defining the width of the exported plot (inches).
height: Numeric value defining the height of the exported plot (inches).

Value

(Invisibly) A ggplot object (or list of ggplot objects, if multiple chunks). If plot=TRUE, the plot(s) are also shown in the Plots pane.