plot_protein: Plotting the underlying quantitative data for a protein

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

Plotting the underlying quantitative data for a protein

Description

Displays the underlying data for a protein.

Usage

plot_protein(X, main = "", col = NULL, split = 0.6, ...)

Arguments

X	Protein data matrix.
main	Title of the plot.
col	Colors of the rows of the data matrix.
split	Fraction of the plotting area for the main figure. The remaining one is for legend. Set this parameter to NULL to ignore the legend area.
...	Additional parameters for plotting.

Value

A NULL value is returned.

Author(s)

Thang V. Pham

References

Pham TV, Tran CTM, Henneman AA, Pham LHC, Le DG, Can AH, Bui PHL, Piersma SR, Jimenez CR. Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics. Journal of Proteome Research 2026 Feb 6; 25(2):1198–1203.

Pham TV, Henneman AA, Jimenez CR. iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. Bioinformatics 2020 Apr 15;36(8):2611-2613.

Examples

data("spikeins")
head(spikeins)
# This example set of spike-in proteins has been 'median-normalized'.
norm_data <- iq::preprocess(spikeins, median_normalization = FALSE, pdf_out = NULL)
protein_list <- iq::create_protein_list(norm_data)
iq::plot_protein(protein_list$P00366, main = "Protein P00366", split = NULL)

iq documentation built on Oct. 28, 2026, 1:07 a.m.