plot_feature: Plotting Individual Protein (Feature)

In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

Description

The simplest way to plot an abundace profile.

Usage

plot_feature(
  m,
  feature,
  feature_name_col = NULL,
  color_by = NULL,
  order_by = color_by
)

Arguments

m	MSnSet or ExpressionSet object
feature	Name of the feature to plot. Should be in featureNames(m).
feature_name_col	Name of the column in fData(m) that should contain name of the feature. The default value is NULL and matches feature against featureNames(m).
color_by	One of the varLabels(m) that will be used to color points. Default is no coloring.
order_by	One of the varLabels(m) for ordering points. Defaul is 'color_by'. If no ordering desired use NULL.

Examples

data(cptac_oca)
plot_feature(oca.set, "NP_001077422.1")
plot_feature(oca.set, "NP_001077422.1", color_by = "Batch")
plot_feature(oca.set, "NP_001077422.1", color_by = "Batch", order_by = "iTRAQ_ID")
plot_feature(oca.set, feature = "NP_001077422.1", feature_name_col = "RefSeq", color_by = "Batch")

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.