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_tableto find matches withcol.id.- match.name
The name of a column in
name_tableto assign new names based on matches ofcol.idandmatch.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.