dataProcessPlotsTMT.RdTo illustrate the quantitative data and quality control of MS runs,
dataProcessPlotsTMT takes the quantitative data from converter functions (PDtoMSstatsTMTFormat, MaxQtoMSstatsTMTFormat, SpectroMinetoMSstatsTMTFormat) 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.
dataProcessPlotsTMT( data.peptide, data.summarization, type, 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 = 10, which.Protein = "all", originalPlot = TRUE, summaryPlot = TRUE, address = "" )
| data.peptide | name of the data with peptide level, which can be the output of converter functions( |
|---|---|
| data.summarization | name of the data with protein-level, which can be the output of |
| 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. |
| 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. |
plot or pdf
data(input.pd) quant.msstats <- proteinSummarization(input.pd, method="msstats", global_norm=TRUE, reference_norm=TRUE)#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 4-29 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-33 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-29 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 1-28 #> # of Transitions/Peptide 1-1#> #>#> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 1-30 #> # of Transitions/Peptide 1-1#> #>#> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 2-30 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 4-31 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-30 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 5-30 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-31 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-31 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 1-31 #> # of Transitions/Peptide 1-1#> #>#> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 3-34 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 2-30 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#> #> Summary of Features : #> count #> # of Protein 10 #> # of Peptides/Protein 5-32 #> # of Transitions/Peptide 1-1 #> #> Summary of Samples : #> 0.125 0.5 0.667 1 Norm #> # of MS runs 2 2 2 2 2 #> # of Biological Replicates 1 1 1 1 1 #> # of Technical Replicates 2 2 2 2 2#> #>#>#>#> #>#> #>#> | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%#> #>#>#>#>#>#>#>#>#>#>#>#>## Profile plot dataProcessPlotsTMT(data.peptide=input.pd, data.summarization=quant.msstats, type='ProfilePlot', width = 21, height = 7)#> Warning: Removed 16 rows containing missing values (geom_point).#>#> Warning: Removed 29 rows containing missing values (geom_point).#> Warning: Removed 1 row(s) containing missing values (geom_path).#>#> Warning: Removed 23 rows containing missing values (geom_point).#> Warning: Removed 1 row(s) containing missing values (geom_path).#>#> Warning: Removed 2 rows containing missing values (geom_point).#>#>#> Warning: Removed 52 rows containing missing values (geom_point).#> Warning: Removed 3 row(s) containing missing values (geom_path).#>#> Warning: Removed 2 rows containing missing values (geom_point).#>#> Warning: Removed 2 rows containing missing values (geom_point).#>#> Warning: Removed 8 rows containing missing values (geom_point).#>#> Warning: Removed 6 rows containing missing values (geom_point).#>#> Warning: Removed 16 rows containing missing values (geom_point).#> Warning: Removed 16 rows containing missing values (geom_point).#>#> Warning: Removed 29 rows containing missing values (geom_point).#> Warning: Removed 1 row(s) containing missing values (geom_path).#> Warning: Removed 29 rows containing missing values (geom_point).#>#> Warning: Removed 23 rows containing missing values (geom_point).#> Warning: Removed 1 row(s) containing missing values (geom_path).#> Warning: Removed 23 rows containing missing values (geom_point).#>#> Warning: Removed 2 rows containing missing values (geom_point).#> Warning: Removed 2 rows containing missing values (geom_point).#>#>#> Warning: Removed 52 rows containing missing values (geom_point).#> Warning: Removed 3 row(s) containing missing values (geom_path).#> Warning: Removed 52 rows containing missing values (geom_point).#>#> Warning: Removed 2 rows containing missing values (geom_point).#> Warning: Removed 2 rows containing missing values (geom_point).#>#> Warning: Removed 2 rows containing missing values (geom_point).#> Warning: Removed 2 rows containing missing values (geom_point).#>#> Warning: Removed 8 rows containing missing values (geom_point).#> Warning: Removed 8 rows containing missing values (geom_point).#>#> Warning: Removed 6 rows containing missing values (geom_point).#> Warning: Removed 6 rows containing missing values (geom_point).#>## NottoRun: QC plot # dataProcessPlotsTMT(data.peptide=input.pd, # data.summarization=quant.msstats, # type='QCPlot', # width = 21, # height = 7)