prot.plot_bar: Plot bar plots for protein abundance or fold change

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Plot bar plots for protein abundance or fold change

Description

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,
  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", "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.
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.
width	Numeric value defining the width of the exported plot.
height	Numeric value defining the height of the exported plot.

Value

(invisibly) a ggplot object as well as the plot in the Plots pane if plot = TRUE.

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.