groupComparisonPlotsPTM: Visualization for model-based analysis and summarization

In devonjkohler/MSstatsPTM: Statistical Characterization of Post-translational Modifications

Description

To analyze the results of modeling changes in abundance of modified peptides and overall protein, groupComparisonPlotsPTM takes as input the results of the groupComparisonPTM function. It asses the results of three models: unadjusted PTM, adjusted PTM, and overall protein. To asses the results of the model, the following visualizations can be created: (1) VolcanoPlot (specify "VolcanoPlot" in option type), to plot peptides or proteins and their significance for each model. (2) Heatmap (specify "Heatmap" in option type), to evaluate the fold change between conditions and peptides/proteins

Usage

groupComparisonPlotsPTM(
  data = data,
  type,
  sig = 0.05,
  FCcutoff = FALSE,
  logBase.pvalue = 10,
  ylimUp = FALSE,
  ylimDown = FALSE,
  xlimUp = FALSE,
  x.axis.size = 10,
  y.axis.size = 10,
  dot.size = 3,
  text.size = 4,
  text.angle = 0,
  legend.size = 13,
  ProteinName = TRUE,
  colorkey = TRUE,
  numProtein = 50,
  width = 10,
  height = 10,
  which.Comparison = "all",
  which.PTM = "all",
  address = ""
)

Arguments

data	name of the list with models, which can be the output of the MSstatsPTM groupComparisonPTM function
type	choice of visualization, one of VolcanoPlot or Heatmap
sig	FDR cutoff for the adjusted p-values in heatmap and volcano plot. level of significance for comparison plot. 100(1-sig)% confidence interval will be drawn. sig=0.05 is default.
FCcutoff	For volcano plot or heatmap, whether involve fold change cutoff or not. FALSE (default) means no fold change cutoff is applied for significance analysis. FCcutoff = specific value means specific fold change cutoff is applied.
logBase.pvalue	for volcano plot or heatmap, (-) logarithm transformation of adjusted p-value with base 2 or 10(default).
ylimUp	for all three plots, upper limit for y-axis. FALSE (default) for volcano plot/heatmap use maximum of -log2 (adjusted p-value) or -log10 (adjusted p-value). FALSE (default) for comparison plot uses maximum of log-fold change + CI.
ylimDown	for all three plots, lower limit for y-axis. FALSE (default) for volcano plot/heatmap use minimum of -log2 (adjusted p-value) or -log10 (adjusted p-value). FALSE (default) for comparison plot uses minimum of log-fold change - CI.
xlimUp	for Volcano plot, the limit for x-axis. FALSE (default) for use maximum for absolute value of log-fold change or 3 as default if maximum for absolute value of log-fold change is less than 3.
x.axis.size	size of axes labels, e.g. name of the comparisons in heatmap, and in comparison plot. Default is 10.
y.axis.size	size of axes labels, e.g. name of targeted proteins in heatmap. Default is 10.
dot.size	size of dots in volcano plot and comparison plot. Default is 3.
text.size	size of ProteinName label in the graph for Volcano Plot. Default is 4.
text.angle	angle of x-axis labels represented each comparison at the bottom of graph in comparison plot. Default is 0.
legend.size	size of legend for color at the bottom of volcano plot. Default is 7.
ProteinName	for volcano plot only, whether display protein names or not. TRUE (default) means protein names, which are significant, are displayed next to the points. FALSE means no protein names are displayed.
colorkey	TRUE(default) shows colorkey.
numProtein	The number of proteins which will be presented in each heatmap. Default is 50.
width	width of the saved file. Default is 10.
height	height of the saved file. Default is 10.
which.Comparison	list of comparisons to draw plots. List can be labels of comparisons or order numbers of comparisons from levels(data$Label) , such as levels(testResultMultiComparisons$ComparisonResult$Label). Default is "all", which generates all plots for each protein.
which.PTM	Protein list to draw comparison plots. List can be names of Proteins or order numbers of Proteins from levels(testResultMultiComparisons$ComparisonResult$Protein). Default is "all", which generates all comparison plots for each protein.
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

model.lf.msstatsptm <- groupComparisonPTM(summary.data, 
                                     data.type = "LabelFree")
groupComparisonPlotsPTM(data = model.lf.msstatsptm,
                        type = "VolcanoPlot",
                        FCcutoff= 2,
                        logBase.pvalue = 2,
                        address=FALSE)

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