## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, warning = FALSE, comment = "#>" ) ## ----install, eval = FALSE---------------------------------------------------- # # install.packages("devtools") # devtools::install_github("svalvaro/MQmetrics") ## ----MQPathCombined----------------------------------------------------------- MQPathCombined <- '/home/alvaro/Documents/MaxQuant/example5/combined/' ## ----report, message=FALSE---------------------------------------------------- library(MQmetrics) ## ----report_question_mark, eval=FALSE----------------------------------------- # ?generateReport ## ----parameters, eval=FALSE--------------------------------------------------- # generateReport(MQPathCombined = , # directory to the combined folder # output_dir = , # directory to store the resulting pdf # long_names = , # If your samples have long names set it to TRUE # sep_names = , # Indicate the separator of those long names # UniprotID = , # Introduce the UniprotID of a protein of interest # intensity_type = ,) # Intensity or LFQ # # # The only mandatory parameter is MQPathCombined, the rest are optional. ## ----example,eval=FALSE------------------------------------------------------- # # If you're using a Unix-like OS use forward slashes. # MQPathCombined <- '/home/alvaro/Documents/MaxQuant/example5/combined/' # # # If you're using Windows you can also use forward slashes: # MQPathCombined <- "D:/Documents/MaxQuant_results/example5/combined/" # # #Use the generateReport function. # generateReport(MQPathCombined) ## ----message=FALSE, warning=FALSE--------------------------------------------- # To create the vignettes and examples I use data that is in the package itself: MQPathCombined <- system.file('extdata/combined/', package = 'MQmetrics') # make_MQCombined will read the tables needed for creating the outputs. MQCombined <- make_MQCombined(MQPathCombined, remove_contaminants = TRUE) ## ----ExperimentDuration, comment= NA------------------------------------------ MaxQuantAnalysisInfo(MQCombined) ## ----PlotProteins,fig.height=5, fig.width=7.2--------------------------------- PlotProteinsIdentified(MQCombined, long_names = TRUE, sep_names = '_', intensity_type = 'LFQ', palette = 'Set2') ## ----PeptidesIdentified, warning=FALSE , fig.height=5, fig.width=7.2---------- PlotPeptidesIdentified(MQCombined, long_names = TRUE, sep_names = '_', palette = 'Set3') ## ----ratio, warning=FALSE , fig.height=5, fig.width=7.2----------------------- PlotProteinPeptideRatio(MQCombined, intensity_type = 'LFQ', long_names = TRUE, sep_names = '_') ## ----PlotMSMS, fig.height=5, fig.width=7.2------------------------------------ PlotMsMs(MQCombined, long_names = TRUE, sep_names = '_', position_dodge_width = 1, palette = 'Set2') ## ----PlotPeaks, fig.height=5, fig.width=7.2----------------------------------- PlotPeaks(MQCombined, long_names = TRUE, sep_names = '_', palette = 'Set2') ## ----isotope, fig.height=5, fig.width=7.2------------------------------------- PlotIsotopePattern(MQCombined, long_names = TRUE, sep_names = '_', palette = 'Set2') ## ----Charg, warning=FALSE, message=FALSE, fig.height=10, fig.width=7.2-------- PlotCharge(MQCombined, palette = 'Set2', plots_per_page = 6) ## ----missed_cleavages,fig.height=10, fig.width=7.2---------------------------- PlotProteaseSpecificity(MQCombined, palette = 'Set2', plots_per_page = 6) ## ----PlotHydrophobicity, warning= F, message= F,fig.height=10, fig.width=7.2---- PlotHydrophobicity(MQCombined, show_median = TRUE, binwidth = 0.1, size_median = 1.5, palette = 'Set2', plots_per_page = 6) ## ----AndromedaScore, message = F, warning = FALSE,fig.height=10, fig.width=7.2---- PlotAndromedaScore(MQCombined, palette = 'Set2', plots_per_page = 6) ## ----PlotIntensity, warning = FALSE, fig.height=5, fig.width=7.2-------------- PlotIntensity(MQCombined, split_violin_intensity = TRUE, intensity_type = 'LFQ', log_base = 2, long_names = TRUE, sep_names = '_', palette = 'Set2') ## ----PlotPCA, warning = FALSE, fig.height=5, fig.width=7.2-------------------- PlotPCA(MQCombined, intensity_type = 'LFQ', palette = 'Set2') ## ----DynamicRange, fig.height=5, fig.width=7.2-------------------------------- PlotCombinedDynamicRange(MQCombined, show_shade = TRUE, percent_proteins = 0.90) ## ----DynamicRangeAll, fig.height=10, fig.width=7.2---------------------------- PlotAllDynamicRange(MQCombined, show_shade = TRUE, percent_proteins = 0.90) ## ----protein_coverage_all, fig.height=7.2, fig.width=7.2---------------------- PlotProteinOverlap(MQCombined) ## ----protein_degradation,fig.height=12, fig.width=12, message=FALSE, warning=F---- PlotProteinCoverage(MQCombined, UniprotID = c('P55072', 'P13639'), log_base = 2, segment_width = 1, palette = 'Set2', plots_per_page = 6) ## ----irt_peps1, warning = FALSE, message= FALSE, fig.height=10, fig.width=7.2---- PlotiRT(MQCombined, show_calibrated_rt = FALSE, tolerance = 0.001, plots_per_page = 6) ## ----irt_peps2, warning = FALSE, message= FALSE, fig.height=10, fig.width=7.2---- PlotiRTScore(MQCombined, tolerance = 0.001, plots_per_page = 6) ## ----TotalIonCurrent, fig.height=10, fig.width=7.2---------------------------- PlotTotalIonCurrent(MQCombined, show_max_value = TRUE, palette = 'Set2', plots_per_page = 6) ## ----Pn, fig.height= 10, warning=F, message=F,fig.height=10, fig.width=7.2---- PlotAcquisitionCycle(MQCombined, palette = 'Set2', plots_per_page = 6) ## ----PTM, fig.height=8, fig.width=7.2----------------------------------------- PlotPTM(MQCombined, peptides_modified = 1, plot_unmodified_peptides = FALSE, palette = 'Set2', aggregate_PTMs = TRUE, plots_per_page = 6) ## ----ptm_single, fig.height=8, fig.width=7.2---------------------------------- PlotPTMAcrossSamples(MQCombined, PTM_of_interest = c('Acetyl (Protein N-term)', 'Oxidation (M)'), long_names = TRUE, sep_names = '_') ## ----report_tables, message=FALSE--------------------------------------------- ReportTables(MQCombined, log_base = 2, intensity_type = 'Intensity') ## ----add_session_info--------------------------------------------------------- sessionInfo()