PCAPlotLiP: Visualize PCA analysis for LiP and TrP datasets.

In devonjkohler/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Description

Takes as input LiP and TrP data from summarization function dataSummarizationLiP. Runs PCA on the summarized data. Can visualize the PCA analysis in three different plots: (1) BarPlot (specify "bar.plot=TRUE" in option bar.plot), to plot a bar plot showing the explained variance per PCA component (2) Peptide/Protein PCA (specify "protein.pca = TRUE" in option protein.pca), to create a dot plot with PCA component 1 and 2 on the axis, for different peptides and proteins. (3) Comparison PCA (specify "comparison.pca = TRUE" in option comparison.pca) , to create a arrow plot with PCA component 1 and 2 on the axis, for different comparisons

Usage

PCAPlotLiP(
  data,
  center.pca = TRUE,
  scale.pca = TRUE,
  n.components = 10,
  bar.plot = TRUE,
  protein.pca = TRUE,
  comparison.pca = FALSE,
  which.pep = "all",
  which.comparison = "all",
  width = 10,
  height = 10,
  address = ""
)

Arguments

data	data name of the list with LiP and (optionally) Protein data, which can be the output of the MSstatsLiP. dataSummarizationLiP function.
center.pca	a logical value indicating whether the variables should be shifted to be zero centered. Alternately, a vector of length equal the number of columns of x can be supplied. The value is passed to scale
scale.pca	a logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place. The default is FALSE for consistency with S, but in general scaling is advisable. Alternatively, a vector of length equal the number of columns of x can be supplied. The value is passed to scale.
n.components	an integer of PCA components to be returned. Default is 10.
bar.plot	a logical value indicating if to visualize PCA bar plot
protein.pca	a logical value indicating if to visualize PCA peptide plot
comparison.pca	a logical value indicating if to visualize PCA comparison plot
which.pep	a list of peptides to be visualized. Default is "all". If too many peptides are plotted the names can overlap.
which.comparison	a list of comparisons to be visualized. Default is "all".
width	width of the saved file. Default is 10.
height	height of the saved file. Default is 10.
address	the name of folder that will store the results. Default folder is the current working directory. The other assigned folder has to be existed under the current working directory. An output pdf file is automatically created with the default name of "VolcanoPlot.pdf" or "Heatmap.pdf". The command address can help to specify where to store the file as well as how to modify the beginning of the file name. If address=FALSE, plot will be not saved as pdf file but showed in window

Value

plot or pdf

Examples

# Use output of dataSummarizationLiP function

# BarPlot
PCAPlotLiP(MSstatsLiP_Summarized, bar.plot = TRUE, protein.pca = FALSE)

# Protein/Peptide PCA Plot
PCAPlotLiP(MSstatsLiP_Summarized, bar.plot = FALSE, protein.pca = TRUE)

# Condition PCA Plot
PCAPlotLiP(MSstatsLiP_Summarized, bar.plot = FALSE, protein.pca = FALSE,
           comparison.pca = TRUE)

devonjkohler/MSstatsLiP documentation built on Dec. 19, 2021, 11:01 p.m.