Visualization for explanatory data analysis

To illustrate the quantitative data and quality control of MS runs, dataProcessPlotsPTM takes the quantitative data from dataSummarizationPTM or dataSummarizationPTM_TMT to plot the following : (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.

dataProcessPlotsPTM(
  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,
  ptm.title = "All PTMs",
  protein.title = "All Proteins",
  which.PTM = "all",
  which.Protein = NULL,
  originalPlot = TRUE,
  summaryPlot = TRUE,
  address = ""
)

Arguments

data	name of the list with PTM and (optionally) Protein data, which can be the output of the MSstatsPTM dataSummarizationPTM or dataSummarizationPTM_TMT functions.
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.
ptm.title	title of overall PTM QC plot
protein.title	title of overall Protein QC plot
which.PTM	PTM list to draw plots. List can be names of PTMs or order numbers of PTMs. Default is "all", which generates all plots for each protein. For QC plot, "allonly" will generate one QC plot with all proteins.
which.Protein	List of proteins to plot. Will plot all PTMs associated with listed Proteins. Default is NULL which will default to which.PTM.
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

# QCPlot
dataProcessPlotsPTM(summary.data,
                    type = 'QCPLOT',
                    which.PTM = "allonly",
                    address = FALSE)
#> Drew the Quality Contol plot(boxplot) for all ptms/proteins.
                    
#ProfilePlot
dataProcessPlotsPTM(summary.data,
                    type = 'PROFILEPLOT',
                    which.PTM = "Q9UQ80_K376",
                    address = FALSE)
#> Warning: Ignoring unknown aesthetics: linetype
#> Warning: Ignoring unknown aesthetics: linetype
#> Drew the Profile plot for Q9UQ80_K376 (1 of 1)
#> Warning: Ignoring unknown aesthetics: linetype
#> Warning: Ignoring unknown aesthetics: linetype
#> Drew the Profile plot for  Q9UQ80_K376 ( 1  of  1 )