Basic R-Usage Guide for PTXQC

This vignette serves as a quickstart guide for R users to create a report from within R using PTXQC.

Target Audience: R users

Reports can be generated using the default configuration of PTXQC. See

vignette("PTXQC-InputData", package = "PTXQC")

how a txt folder should look like.

Generate a default report

This is the most simple invokation of PTXQC::createReport().

require(PTXQC)
## Loading required package: PTXQC
## Loading package PTXQC (version 0.92.3)
## the next require() is needed to prevent a spurious error in certain R versions (might be a bug in R or a package)
## error message is:
##    Error in Scales$new : could not find function "loadMethod"
require(methods)

## specify a path to a MaxQuant txt folder
## Note: This folder needs to be complete (see 'vignette("PTXQC-InputData", package = "PTXQC")')
if (1) {
  ## we will use an example dataset from PRIDE (dataset 2 of the PTXQC publication)
  local_zip = tempfile(fileext=".zip")
  tryCatch({
    download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", destfile = local_zip)
  }, error = function(err) {
    ## on Windows, one can get a 'cannot open URL' using the default method. So we try another
    download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", destfile = local_zip, method= "internal")
  })
  unzip(local_zip, exdir = tempdir()) ## extracts content
  txt_folder = file.path(tempdir(), "txt_20min")
} else {
  ## if you have local MaxQuant output, just use it
  txt_folder = "c:/Proteomics/MouseLiver/combined/txt"
}
## Warning in download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", : InternetOpenUrl failed: 'The login request was denied
## '
r = createReport(txt_folder)
## YAML: PTXQC$ReportFilename$extended def: TRUE
## YAML: PTXQC$UseLocalMQPar def: TRUE
## YAML: File$Parameters$enabled def: TRUE
## YAML: PTXQC$NameLengthMax_num def: 10
## YAML: File$Summary$enabled def: TRUE
## YAML: File$Summary$IDRate$Thresh_bad_num def: 20
## YAML: File$Summary$IDRate$Thresh_great_num def: 35
## YAML: File$ProteinGroups$enabled def: TRUE
## YAML: File$ProteinGroups$RatioPlot$LabelIncThresh_num def: 4
## YAML: File$ProteinGroups$IntensityThreshLog2_num def: 25
## YAML: File$Evidence$enabled def: TRUE
## YAML: File$Evidence$ProteinCountThresh_num def: 3500
## YAML: File$Evidence$IntensityThreshLog2_num def: 23
## YAML: File$Evidence$PeptideCountThresh_num def: 15000
## YAML: File$Evidence$SpecialContaminants def: c("MYCOPLASMA", "1")
## YAML: File$Evidence$MQpar_MatchingTimeWindow_num def: 1
## YAML: File$Evidence$MatchBetweenRuns_wA def: auto
## YAML: File$Evidence$MQpar_firstSearchTol_num def: 20
## YAML: File$Evidence$firstSearch_outOfCalWarnSD_num def: 2
## YAML: File$Evidence$MQpar_mainSearchTol_num def: NA
## YAML: File$MsMs$enabled def: TRUE
## YAML: File$MsMsScans$enabled def: TRUE
## YAML: File$MsMsScans$IonInjectionThresh_num def: 10
## YAML: PTXQC$OutputFormats def: html,plainPDF
## YAML: PTXQC$PlainPDF$AddPageNumbers def: on
## YAML: order$qcMetric_PAR def: 1
## YAML: order$qcMetric_PG_PCA def: 3
## YAML: order$qcMetric_EVD_Top5Cont def: 10
## YAML: order$qcMetric_PG_Ratio def: 19
## YAML: order$qcMetric_EVD_UserContaminant def: 20
## YAML: order$qcMetric_EVD_PeptideInt def: 30
## YAML: order$qcMetric_EVD_ReporterInt def: 31
## YAML: order$qcMetric_PG_RawInt def: 32
## YAML: order$qcMetric_PG_LFQInt def: 33
## YAML: order$qcMetric_PG_ReporterInt def: 34
## YAML: order$qcMetric_MSMS_MissedCleavages def: 40
## YAML: order$qcMetric_EVD_Charge def: 100
## YAML: order$qcMetric_PG_Cont def: 110
## YAML: order$qcMetric_MSMSScans_TopNoverRT def: 120
## YAML: order$qcMetric_EVD_IDoverRT def: 150
## YAML: order$qcMetric_EVD_RTPeakWidth def: 170
## YAML: order$qcMetric_EVD_MBRAlign def: 210
## YAML: order$qcMetric_EVD_MBRIdTransfer def: 220
## YAML: order$qcMetric_EVD_MBRaux def: 221
## YAML: order$qcMetric_MSMSScans_IonInjTime def: 240
## YAML: order$qcMetric_MSMSScans_MSMSIntensity def: 245
## YAML: order$qcMetric_EVD_MS2OverSampling def: 250
## YAML: order$qcMetric_EVD_PreCal def: 260
## YAML: order$qcMetric_EVD_PostCal def: 270
## YAML: order$qcMetric_MSMS_MSMSDecal def: 280
## YAML: order$qcMetric_SM_MSMSIdRate def: 300
## YAML: order$qcMetric_MSMSScans_TopN def: 350 || new val: 120
## YAML: order$qcMetric_MSMSScans_TopNID def: 380
## YAML: order$qcMetric_MSMSScans_DepPep def: 383
## YAML: order$qcMetric_EVD_MissingValues def: 390
## YAML: order$qcMetric_EVD_PeptideCount def: 400
## YAML: order$qcMetric_EVD_ProteinCount def: 450
## YAML: order$qcMetric_AverageQualOverall def: 9999
## Reading file C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/parameters.txt ...
## Read 61 entries from C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/parameters.txt.
## Updating colnames
## Simplifying contaminants
## Simplifying reverse
## Starting to work on PAR: MQ Parameters ...
## 
## Memory [MB] prior|after|max(diff) : 52 | 53.7 | 88.4 (36)
## 
## Duration: 0 s
## 
## ... PAR: MQ Parameters  done
## Reading file C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/summary.txt ...
## Read 9 entries from C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/summary.txt.
## Updating colnames
## Simplifying contaminants
## Simplifying reverse
## Adding fc.raw.file column ... done
## Starting to work on SM: MS^2 ID rate (">%1.0f") ...
## 
## Memory [MB] prior|after|max(diff) : 54 | 55.4 | 78 (24)
## 
## Duration: 0 s
## 
## ... SM: MS^2 ID rate (">%1.0f")  done
## Reading file C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/proteinGroups.txt ...
## Read 4134 entries from C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/proteinGroups.txt.
## Updating colnames
## Simplifying contaminants
## Simplifying reverse
## Starting to work on PG: Contaminants ...
## 
## Memory [MB] prior|after|max(diff) : 62.5 | 63.1 | 82 (19)
## 
## Duration: 0 s
## 
## ... PG: Contaminants  done
## Starting to work on PG: raw intensity ...
## 
## Memory [MB] prior|after|max(diff) : 63.1 | 65.4 | 106 (43)
## 
## Duration: 0 s
## 
## ... PG: raw intensity  done
## Starting to work on PG: LFQ intensity ...
## 
## Memory [MB] prior|after|max(diff) : 65.4 | 66.3 | 97.6 (32)
## 
## Duration: 0 s
## 
## ... PG: LFQ intensity  done
## Starting to work on PG: Principal Component ...
## 
## Memory [MB] prior|after|max(diff) : 66.3 | 67.7 | 117.7 (51)
## 
## Duration: 0 s
## 
## ... PG: Principal Component  done
## Reading file C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/evidence.txt ...
## Requiring column(s) 'retention.length' to be of type 'numeric'!
## Requiring column(s) 'retention.time.calibration' to be of type 'numeric'!
## Requiring column(s) 'retention.time', 'calibrated.retention.time' to be of type 'numeric'!
## Requiring column(s) 'match.time.difference' to be of type 'numeric'!
## Requiring column(s) 'intensity' to be of type 'numeric'!
## Requiring column(s) 'mass.error..ppm.', 'mass.error..da.', 'uncalibrated.mass.error..ppm.', 'uncalibrated.mass.error..da.' to be of type 'numeric'!
## Requiring column(s) 'uncalibrated...calibrated.m.z..ppm.', 'uncalibrated...calibrated.m.z..da.' to be of type 'numeric'!
## Requiring column(s) 'm.z' to be of type 'numeric'!
## Requiring column(s) 'score' to be of type 'numeric'!
## WARNING: Could not find column regex '^fraction$' using case-INsensitive matching.
## WARNING: Could not find column regex '[RK]\.Count' using case-INsensitive matching.
## Requiring column(s) 'charge' to be of type 'numeric'!
## Requiring column(s) 'mass' to be of type 'numeric'!
## Requiring column(s) 'ms.ms.count' to be of type 'numeric'!
## WARNING: Could not find column regex '^reporter.intensity.' using case-INsensitive matching.
## Keeping 17 of 62 columns!
## Read 90398 entries from C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/evidence.txt.
## Updating colnames
## Simplifying contaminants
## Simplifying reverse
## Adding fc.raw.file column ... done
## Starting to work on EVD:Contaminant (%s) ...
## 
## Memory [MB] prior|after|max(diff) : 88.5 | 89.6 | 143.6 (55)
## 
## Duration: 0 s
## 
## ... EVD:Contaminant (%s)  done
## Starting to work on EVD: Pep Intensity (">%1.1f") ...
## 
## Memory [MB] prior|after|max(diff) : 89.6 | 99.4 | 142.4 (53)
## 
## Duration: 0 s
## 
## ... EVD: Pep Intensity (">%1.1f")  done
## Starting to work on EVD: Prot Count (">%1.0f") ...
## 
## Memory [MB] prior|after|max(diff) : 99.8 | 100 | 156.3 (56)
## 
## Duration: 0 s
## 
## ... EVD: Prot Count (">%1.0f")  done
## Starting to work on EVD: Pep Count (">%1.0f") ...
## 
## Memory [MB] prior|after|max(diff) : 100 | 100.2 | 133.5 (34)
## 
## Duration: 0 s
## 
## ... EVD: Pep Count (">%1.0f")  done
## Starting to work on EVD: RT Peak Width ...
## 
## Memory [MB] prior|after|max(diff) : 100.2 | 100.4 | 173.6 (73)
## 
## Duration: 0 s
## 
## ... EVD: RT Peak Width  done
## Starting to work on EVD: MBR Align ...
## 
## Memory [MB] prior|after|max(diff) : 100.4 | 101.8 | 173.8 (73)
## 
## Duration: 5 s
## 
## ... EVD: MBR Align  done
## Starting to work on EVD: MBR ID-Transfer ...
## 
## Memory [MB] prior|after|max(diff) : 101.8 | 102.4 | 310 (208)
## 
## Duration: 42 s
## 
## ... EVD: MBR ID-Transfer  done
## Starting to work on EVD: MBR auxilliary ...
## 
## Memory [MB] prior|after|max(diff) : 102.4 | 107.8 | 261.9 (160)
## 
## Duration: 1 s
## 
## ... EVD: MBR auxilliary  done
## Starting to work on EVD: Charge ...
## Warning: Ignoring unknown aesthetics: width
## 
## Memory [MB] prior|after|max(diff) : 107.8 | 108 | 138 (30)
## 
## Duration: 0 s
## 
## ... EVD: Charge  done
## Starting to work on EVD: ID rate over RT ...
## 
## Memory [MB] prior|after|max(diff) : 108 | 108.2 | 177.2 (69)
## 
## Duration: 0 s
## 
## ... EVD: ID rate over RT  done
## Starting to work on EVD: MS Cal-Pre (%1.1f) ...
## 
## Memory [MB] prior|after|max(diff) : 108.2 | 111.5 | 205.5 (97)
## 
## Duration: 0 s
## 
## ... EVD: MS Cal-Pre (%1.1f)  done
## Starting to work on EVD: MS Cal-Post ...
## 
## Memory [MB] prior|after|max(diff) : 111.5 | 114.8 | 218.4 (107)
## 
## Duration: 0 s
## 
## ... EVD: MS Cal-Post  done
## Starting to work on EVD: Contaminants ...
## 
## Memory [MB] prior|after|max(diff) : 114.8 | 117.8 | 194.5 (80)
## 
## Duration: 0 s
## 
## ... EVD: Contaminants  done
## Starting to work on EVD: MS^2 Oversampling ...
## 
## Memory [MB] prior|after|max(diff) : 117.8 | 118 | 171 (53)
## 
## Duration: 0 s
## 
## ... EVD: MS^2 Oversampling  done
## Starting to work on EVD: Pep Missing Values ...
## 
## Memory [MB] prior|after|max(diff) : 118 | 125.6 | 309.4 (191)
## 
## Duration: 1 s
## 
## ... EVD: Pep Missing Values  done
## Reading file C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/msms.txt ...
## Requiring column(s) 'missed.cleavages' to be of type 'numeric'!
## Requiring column(s) 'evidence.id' to be of type 'numeric'!
## Keeping 2 of 60 columns!
## Read 86086 entries from C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/msms.txt.
## Updating colnames
## Simplifying contaminants
## Simplifying reverse
## Adding fc.raw.file column ... done
## Starting to work on MSMS: MS^2 Cal (%s) ...
## 
## Memory [MB] prior|after|max(diff) : 222.2 | 225.8 | 300.9 (79)
## 
## Duration: 1 s
## 
## ... MSMS: MS^2 Cal (%s)  done
## Starting to work on MSMS: %s ...
## 
## Memory [MB] prior|after|max(diff) : 225.8 | 226 | 258 (32)
## 
## Duration: 0 s
## 
## ... MSMS: %s  done
## Reading file C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/msmsScans.txt ...
## Requiring column(s) 'ion.injection.time' to be of type 'numeric'!
## Requiring column(s) 'retention.time' to be of type 'numeric'!
## WARNING: Could not find column regex '^dp.aa$' using case-INsensitive matching.
## WARNING: Could not find column regex '^dp.modification$' using case-INsensitive matching.
## Keeping 2 of 41 columns!
## Read 201567 entries from C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/msmsScans.txt.
## Updating colnames
## Simplifying contaminants
## Simplifying reverse
## Adding fc.raw.file column ... done
## Starting to work on MS^2*Scans: TopN over RT ...
## 
## Memory [MB] prior|after|max(diff) : 141.7 | 143.7 | 243.2 (102)
## 
## Duration: 0 s
## 
## ... MS^2*Scans: TopN over RT  done
## Starting to work on MS^2*Scans: Ion Inj Time ...
## 
## Memory [MB] prior|after|max(diff) : 143.6 | 144.1 | 159.8 (16)
## 
## Duration: 0 s
## 
## ... MS^2*Scans: Ion Inj Time  done
## Starting to work on MS^2*Scans: Intensity ...
## Warning: Ignoring unknown aesthetics: width
## 
## Memory [MB] prior|after|max(diff) : 143.8 | 151.5 | 231.3 (88)
## 
## Duration: 0 s
## 
## ... MS^2*Scans: Intensity  done
## Starting to work on MS^2*Scans: TopN high ...
## 
## Memory [MB] prior|after|max(diff) : 151.3 | 151.4 | 175.4 (24)
## 
## Duration: 0 s
## 
## ... MS^2*Scans: TopN high  done
## Starting to work on MS^2*Scans: TopN ID over N ...
## 
## Memory [MB] prior|after|max(diff) : 151.3 | 151.4 | 172.2 (21)
## 
## Duration: 0 s
## 
## ... MS^2*Scans: TopN ID over N  done
## [1] "#Metrics: "
## [1] 33
## Starting to work on Average Overall Quality ...
## 
## Memory [MB] prior|after|max(diff) : 151.5 | 151.5 | 152.5 (1)
## 
## Duration: 0 s
## 
## ... Average Overall Quality  done
## Warning in FUN(subset, ...): NAs introduced by coercion
## Creating Report file ...HTML TEMPLATE: C:/Users/bielow/AppData/Local/Temp/RtmpEzO9PV/Rinst10147a5875f6/PTXQC/./reportTemplate/PTXQC_report_template.Rmd
## processing file: PTXQC_report_template.Rmd
## Warning: Removed 1342 rows containing non-finite values (stat_boxplot).
## Warning: position_dodge requires non-overlapping x intervals
## Warning: Removed 85 rows containing non-finite values (stat_boxplot).
## Warning: position_dodge requires non-overlapping x intervals
## Warning: Removed 125 rows containing non-finite values (stat_boxplot).
## Warning: position_dodge requires non-overlapping x intervals
## Warning: Removed 5 rows containing missing values (geom_point).
## Warning: Removed 719 rows containing non-finite values (stat_boxplot).
## Warning: Removed 779 rows containing non-finite values (stat_boxplot).
## Warning: Removed 720 rows containing non-finite values (stat_bin).
## Warning: Removed 719 rows containing non-finite values (stat_bin).
## output file: PTXQC_report_template.knit.md
## "C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS PTXQC_report_template.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output pandocbac2f222cea.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\bielow\Documents\R\win-library\3.4\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --number-sections --variable "theme:bootstrap" --include-in-header "C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2\rmarkdown-strbac488c610b.html"
## 
## Output created: C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/report_v0.92.3_txt_20min.html
## [[1]]
## Warning: Removed 4 rows containing missing values (geom_text).
## Warning: Removed 1342 rows containing non-finite values (stat_boxplot).
## Warning: position_dodge requires non-overlapping x intervals
## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font
## metrics unknown for character 0xa

## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font
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## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
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## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
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## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
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## Warning: Removed 85 rows containing non-finite values (stat_boxplot).
## Warning: position_dodge requires non-overlapping x intervals
## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font
## metrics unknown for character 0xa

## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font
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## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa
## Warning: Removed 125 rows containing non-finite values (stat_boxplot).
## Warning: position_dodge requires non-overlapping x intervals
## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font
## metrics unknown for character 0xa

## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font
## metrics unknown for character 0xa
## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa

## Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa

## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa
## Warning: Removed 5 rows containing missing values (geom_point).
## Warning: Removed 719 rows containing non-finite values (stat_boxplot).
## Warning: Removed 779 rows containing non-finite values (stat_boxplot).
## Warning: Removed 720 rows containing non-finite values (stat_bin).
## Warning: Removed 719 rows containing non-finite values (stat_bin).
##  done
## Report file created at
## 
##     C:\Users\bielow\AppData\Local\Temp\Rtmp2dZun2/txt_20min/report_v0.92.3_txt_20min.*
## 
## 
## 
## Time elapsed: 1.8 min
cat(paste0("\nReport generated as '", r$report_file, "'\n\n"))
## 
## Report generated as ''

Generate a customized report

The report can be customized via a YAML configuration file. For details, see

vignette("PTXQC-CustomizeReport", package = "PTXQC")

After editing the YAML configuration to your needs, run the code below.

require(PTXQC)
require(yaml)

## the next require() is needed to prevent a spurious error in certain R versions (might be a bug in R or a package)
## error message is:
##    Error in Scales$new : could not find function "loadMethod"
require(methods)

## specify a path to a MaxQuant txt folder
## Note: This folder can be incomplete, depending on your YAML config
if (1) {
  ## we will use an example dataset from PRIDE (dataset 2 of the PTXQC publication)
  local_zip = tempfile(fileext=".zip")
  download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", destfile = local_zip)
  unzip(local_zip, exdir = tempdir()) ## extracts content
  txt_folder = file.path(tempdir(), "txt_20min")
} else {
  ## if you have local MaxQuant output, just use it
  txt_folder = "c:/Proteomics/MouseLiver/combined/txt"
}

## use a YAML config inside the target directory if present
fh_out = getReportFilenames(txt_folder)
if (file.exists(fh_out$yaml_file))
{
  cat("\nUsing YAML config already present in target directory ...\n")
  yaml_config = yaml.load_file(input = fh_out$yaml_file)
} else {
  cat("\nYAML config not found in folder '", txt_folder, "'. The first run of PTXQC will create one for you.", sep="")
  yaml_config = list()
}

r = createReport(txt_folder, yaml_config)

cat(paste0("\nReport generated as '", r$report_file, "'\n\n"))

That’s it.