dataProcessPlotsTMT: Visualization for explanatory data analysis - TMT experiment

In Vitek-Lab/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Visualization for explanatory data analysis - TMT experiment

Description

To illustrate the quantitative data and quality control of MS runs, dataProcessPlotsTMT takes the quantitative data and summarized data from function 'proteinSummarization' 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 and channels.

Usage

dataProcessPlotsTMT(
  data,
  type,
  featureName = "Transition",
  ylimUp = FALSE,
  ylimDown = FALSE,
  x.axis.size = 10,
  y.axis.size = 10,
  text.size = 2,
  text.angle = 90,
  legend.size = 7,
  dot.size.profile = 2,
  ncol.guide = 5,
  width = 10,
  height = 10,
  which.Protein = "all",
  originalPlot = TRUE,
  summaryPlot = TRUE,
  address = "",
  isPlotly = FALSE
)

Arguments

data	the output of proteinSummarization function. It is a list with data frames 'FeatureLevelData' and 'ProteinLevelData'
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.
featureName	for "ProfilePlot" only, "Transition" (default) means printing feature legend in transition-level; "Peptide" means printing feature legend in peptide-level; "NA" means no feature legend printing. FALSE(Default) for Profile Plot and QC Plot uses the upper limit as rounded off maximum of log2(intensities) after normalization + 3..
ylimUp	upper limit for y-axis in the log scale.
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.
which.Protein	Protein list to draw plots. List can be names of Proteins or order numbers of Proteins. Default is "all", which generates all plots for each protein. For QC plot, "allonly" will generate one QC plot with all proteins.
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.
isPlotly	Parameter to use Plotly or ggplot2. If set to TRUE, MSstats will save Plotly plots as HTML files. If set to FALSE MSstats will save ggplot2 plots as PDF files

Value

plot or pdf

Examples

data(input.pd)
quant.msstats = proteinSummarization(input.pd,
                                      method="msstats",
                                      global_norm=TRUE,
                                      reference_norm=TRUE)

## Profile plot
dataProcessPlotsTMT(data=quant.msstats,
                   type='ProfilePlot',
                   width = 21,
                   height = 7)

## NottoRun: QC plot
# dataProcessPlotsTMT(data=quant.msstats,
                    # type='QCPlot',
                    # width = 21,
                    # height = 7)
                    

Vitek-Lab/MSstatsTMT documentation built on Nov. 18, 2024, 11:30 a.m.