plot_incorporation: Plot annotated histogram of incorporation values

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

Plot annotated histogram of incorporation values

Description

SILAC (2-plex) label incorporation is estimated from the set of observed features (peptides or proteins). If the test sample contains cells grown in 'Heavy' media only, incorporation is simply the mean observed incorporation. If the test sample contains a mixture of 'Heavy' and 'Light', the incorporation is best calculated from the median incorporation using the corrected 'Light' intensity.

Usage

plot_incorporation(
  data,
  incorporation_col = "Incorporation",
  corrected_col = "Incorporation.corrected",
  level = "peptide",
  mix = 0
)

Arguments

data	data.frame containing features with column 'incorporation'. If mix>0, must also contain column 'corrected_incorporation' where incorporation is calculated using the corrected light peptide intensity
incorporation_col	string. Name of the column containing incorporation values which can be calculated with get_incorporation.
corrected_col	string Optional, but required if mix > 0. Name of the column containing mix-corrected incorporation values which can be calculated with get_incorporation.
level	string. Name for feature level, either 'peptide' or 'protein'.
mix	numeric. The 'Heavy' to 'Light' mix ratio. Default is 0, otherwise use a number greater than 0.

Value

Returns a list with p = ggplot plot and incorporation_estimates = list of incorporation estimates.

CambridgeCentreForProteomics/camprotR documentation built on July 7, 2024, 2:13 a.m.