dataProcessPlotsLiP: Visualization for explanatory data analysis

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

Description

To illustrate the quantitative data and quality control of MS runs, dataProcessPlotsLiP takes the quantitative data from MSstatsLiP converter functions as input and generate two types of figures in pdf files as output : (1) profile plot (specify "ProfilePlot" in option type), to identify the potential sources of variation for each protein; (2) quality control plot (specify "QCPlot" in option type), to evaluate the systematic bias between MS runs.

Usage

dataProcessPlotsLiP(
  data,
  type = "PROFILEPLOT",
  ylimUp = FALSE,
  ylimDown = FALSE,
  x.axis.size = 10,
  y.axis.size = 10,
  text.size = 4,
  text.angle = 90,
  legend.size = 7,
  dot.size.profile = 2,
  ncol.guide = 5,
  width = 10,
  height = 12,
  lip.title = "All Peptides",
  protein.title = "All Proteins",
  which.Peptide = "all",
  which.Protein = NULL,
  originalPlot = TRUE,
  summaryPlot = TRUE,
  address = ""
)

Arguments

data	name of the list with LiP and (optionally) Protein data, which can be the output of the MSstatsLiP. dataSummarizationLiP function.
type	choice of visualization. "ProfilePlot" represents profile plot of log intensities across MS runs. "QCPlot" represents box plots of log intensities across channels and MS runs.
ylimUp	upper limit for y-axis in the log scale. FALSE(Default) for Profile Plot and QC Plot uses the upper limit as rounded off maximum of log2(intensities) after normalization + 3..
ylimDown	lower limit for y-axis in the log scale. FALSE(Default) for Profile Plot and QC Plot uses 0..
x.axis.size	size of x-axis labeling for "Run" and "channel in Profile Plot and QC Plot.
y.axis.size	size of y-axis labels. Default is 10.
text.size	size of labels represented each condition at the top of Profile plot and QC plot. Default is 4.
text.angle	angle of labels represented each condition at the top of Profile plot and QC plot. Default is 0.
legend.size	size of legend above Profile plot. Default is 7.
dot.size.profile	size of dots in Profile plot. Default is 2.
ncol.guide	number of columns for legends at the top of plot. Default is 5.
width	width of the saved pdf file. Default is 10.
height	height of the saved pdf file. Default is 10.
lip.title	title of all LiP QC plot
protein.title	title of all Protein QC plot
which.Peptide	LiP peptide list to draw plots. List can be names of LiP peptides or order numbers of LiPs. Default is "all", which generates all plots for each protein. For QC plot, "allonly" will generate one QC plot with all proteins.
which.Protein	String of protein's to plot if the user would like to plot all Peptides associated with a given Protein. Default is NULL. Please do not include "all" or "allonly" here.
originalPlot	TRUE(default) draws original profile plots, without normalization.
summaryPlot	TRUE(default) draws profile plots with protein summarization for each channel and MS run.
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 "ProfilePlot.pdf" or "QCplot.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 the output of the MSstatsLiP_Summarized function
# Profile Plot
dataProcessPlotsLiP(MSstatsLiP_Summarized, type = "ProfilePlot")

# QCPlot Plot
dataProcessPlotsLiP(MSstatsLiP_Summarized, type = "QCPlot")

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