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.
This is the most simple invokation of PTXQC::createReport().
require(PTXQC)## Loading required package: PTXQC## Loading package PTXQC (version 0.92.0)## 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$new : could not find function "loadMethod"
require(methods)
## specify a path to a MaxQuant txt folder
## Note: This folder needs to be complete (see 'vignette("PTXQC-InputData", package = "PTXQC")')
if (1) {
## we will use an example dataset from PRIDE (dataset 2 of the PTXQC publication)
local_zip = tempfile(fileext=".zip")
tryCatch({
download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", destfile = local_zip)
}, error = function(err) {
## on Windows, one can get a 'cannot open URL' using the default method. So we try another
download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", destfile = local_zip, method= "internal")
})
unzip(local_zip, exdir = tempdir()) ## extracts content
txt_folder = file.path(tempdir(), "txt_20min")
} else {
## if you have local MaxQuant output, just use it
txt_folder = "c:/Proteomics/MouseLiver/combined/txt"
}## Warning in download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", : InternetOpenUrl failed: 'The login request was denied
## 'r = createReport(txt_folder)## getYAML with: PTXQC$ReportFilename$extended default: TRUE
## .. return default: TRUE
## getYAML with: PTXQC$UseLocalMQPar default: TRUE
## .. return default: TRUE
## getYAML with: File$Parameters$enabled default: TRUE
## .. return default: TRUE
## getYAML with: PTXQC$NameLengthMax_num default: 10
## .. return default: 10
## getYAML with: File$Summary$enabled default: TRUE
## .. return default: TRUE
## getYAML with: File$Summary$IDRate$Thresh_bad_num default: 20
## .. return default: 20
## getYAML with: File$Summary$IDRate$Thresh_great_num default: 35
## .. return default: 35
## getYAML with: File$ProteinGroups$enabled default: TRUE
## .. return default: TRUE
## getYAML with: File$ProteinGroups$RatioPlot$LabelIncThresh_num default: 4
## .. return default: 4
## getYAML with: File$ProteinGroups$IntensityThreshLog2_num default: 25
## .. return default: 25
## getYAML with: File$Evidence$enabled default: TRUE
## .. return default: TRUE
## getYAML with: File$Evidence$ProteinCountThresh_num default: 3500
## .. return default: 3500
## getYAML with: File$Evidence$IntensityThreshLog2_num default: 23
## .. return default: 23
## getYAML with: File$Evidence$PeptideCountThresh_num default: 15000
## .. return default: 15000
## getYAML with: File$Evidence$SpecialContaminants default: c("MYCOPLASMA", "1")
## .. return default: c("MYCOPLASMA", "1")
## getYAML with: File$Evidence$MQpar_MatchingTimeWindow_num default: 1
## .. return default: 1
## getYAML with: File$Evidence$MatchBetweenRuns_wA default: auto
## .. return default: auto
## getYAML with: File$Evidence$MQpar_firstSearchTol_num default: 20
## .. return default: 20
## getYAML with: File$Evidence$firstSearch_outOfCalWarnSD_num default: 2
## .. return default: 2
## getYAML with: File$Evidence$MQpar_mainSearchTol_num default: NA
## .. return default: NA
## getYAML with: File$MsMs$enabled default: TRUE
## .. return default: TRUE
## getYAML with: File$MsMsScans$enabled default: TRUE
## .. return default: TRUE
## getYAML with: File$MsMsScans$IonInjectionThresh_num default: 10
## .. return default: 10
## getYAML with: PTXQC$OutputFormats default: html
## getYAML with: PTXQC$OutputFormats default: plainPDF
## .. return default: html
## .. return default: plainPDF
## getYAML with: PTXQC$PlainPDF$AddPageNumbers default: on
## .. return default: on
## meta id: qcMetric_PAR
## getYAML with: order$qcMetric_PAR default: 1
## .. return default: 1
## meta id: qcMetric_PG_PCA
## getYAML with: order$qcMetric_PG_PCA default: 3
## .. return default: 3
## meta id: qcMetric_EVD_Top5Cont
## getYAML with: order$qcMetric_EVD_Top5Cont default: 10
## .. return default: 10
## meta id: qcMetric_PG_Ratio
## getYAML with: order$qcMetric_PG_Ratio default: 19
## .. return default: 19
## meta id: qcMetric_EVD_UserContaminant
## getYAML with: order$qcMetric_EVD_UserContaminant default: 20
## .. return default: 20
## meta id: qcMetric_EVD_PeptideInt
## getYAML with: order$qcMetric_EVD_PeptideInt default: 30
## .. return default: 30
## meta id: qcMetric_PG_RawInt
## getYAML with: order$qcMetric_PG_RawInt default: 32
## .. return default: 32
## meta id: qcMetric_PG_LFQInt
## getYAML with: order$qcMetric_PG_LFQInt default: 33
## .. return default: 33
## meta id: qcMetric_PG_ITRAQInt
## getYAML with: order$qcMetric_PG_ITRAQInt default: 34
## .. return default: 34
## meta id: qcMetric_MSMS_MissedCleavages
## getYAML with: order$qcMetric_MSMS_MissedCleavages default: 40
## .. return default: 40
## meta id: qcMetric_EVD_Charge
## getYAML with: order$qcMetric_EVD_Charge default: 100
## .. return default: 100
## meta id: qcMetric_PG_Cont
## getYAML with: order$qcMetric_PG_Cont default: 110
## .. return default: 110
## meta id: qcMetric_MSMSScans_TopNoverRT
## getYAML with: order$qcMetric_MSMSScans_TopNoverRT default: 120
## .. return default: 120
## meta id: qcMetric_EVD_IDoverRT
## getYAML with: order$qcMetric_EVD_IDoverRT default: 150
## .. return default: 150
## meta id: qcMetric_EVD_RTPeakWidth
## getYAML with: order$qcMetric_EVD_RTPeakWidth default: 170
## .. return default: 170
## meta id: qcMetric_EVD_MBRAlign
## getYAML with: order$qcMetric_EVD_MBRAlign default: 210
## .. return default: 210
## meta id: qcMetric_EVD_MBRIdTransfer
## getYAML with: order$qcMetric_EVD_MBRIdTransfer default: 220
## .. return default: 220
## meta id: qcMetric_EVD_MBRaux
## getYAML with: order$qcMetric_EVD_MBRaux default: 221
## .. return default: 221
## meta id: qcMetric_MSMSScans_IonInjTime
## getYAML with: order$qcMetric_MSMSScans_IonInjTime default: 240
## .. return default: 240
## meta id: qcMetric_MSMSScans_MSMSIntensity
## getYAML with: order$qcMetric_MSMSScans_MSMSIntensity default: 245
## .. return default: 245
## meta id: qcMetric_EVD_MS2OverSampling
## getYAML with: order$qcMetric_EVD_MS2OverSampling default: 250
## .. return default: 250
## meta id: qcMetric_EVD_PreCal
## getYAML with: order$qcMetric_EVD_PreCal default: 260
## .. return default: 260
## meta id: qcMetric_EVD_PostCal
## getYAML with: order$qcMetric_EVD_PostCal default: 270
## .. return default: 270
## meta id: qcMetric_MSMS_MSMSDecal
## getYAML with: order$qcMetric_MSMS_MSMSDecal default: 280
## .. return default: 280
## meta id: qcMetric_SM_MSMSIdRate
## getYAML with: order$qcMetric_SM_MSMSIdRate default: 300
## .. return default: 300
## meta id: qcMetric_MSMSScans_TopN
## getYAML with: order$qcMetric_MSMSScans_TopN default: 350
## .. return val: 120
## meta id: qcMetric_MSMSScans_TopNID
## getYAML with: order$qcMetric_MSMSScans_TopNID default: 380
## .. return default: 380
## meta id: qcMetric_MSMSScans_DepPep
## getYAML with: order$qcMetric_MSMSScans_DepPep default: 383
## .. return default: 383
## meta id: qcMetric_EVD_MissingValues
## getYAML with: order$qcMetric_EVD_MissingValues default: 390
## .. return default: 390
## meta id: qcMetric_EVD_PeptideCount
## getYAML with: order$qcMetric_EVD_PeptideCount default: 400
## .. return default: 400
## meta id: qcMetric_EVD_ProteinCount
## getYAML with: order$qcMetric_EVD_ProteinCount default: 450
## .. return default: 450
## meta id: qcMetric_AverageQualOverall
## getYAML with: order$qcMetric_AverageQualOverall default: 9999
## .. return default: 9999
## Reading file C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/txt_20min/parameters.txt ...
## Read 61 entries from C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/txt_20min/parameters.txt.
## Updating colnames
## Simplifying contaminants
## Simplifying reverse
## Starting to work on PAR: MQ Parameters ...
##
## Memory [MB] prior|after|max(diff) : 42.2 | 43.6 | 70.6 (28)
##
## Duration: 0 s
##
## ... PAR: MQ Parameters done
## Reading file C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/txt_20min/summary.txt ...
## Read 9 entries from C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/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) : 43.7 | 45 | 50.1 (6)
##
## Duration: 0 s
##
## ... SM: MS^2 ID rate (">%1.0f") done
## Reading file C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/txt_20min/proteinGroups.txt ...
## Read 4134 entries from C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/txt_20min/proteinGroups.txt.
## Updating colnames
## Simplifying contaminants
## Simplifying reverse
## Starting to work on PG: Contaminants ...
##
## Memory [MB] prior|after|max(diff) : 52.1 | 52.6 | 57.8 (6)
##
## Duration: 0 s
##
## ... PG: Contaminants done
## Starting to work on PG: raw intensity ...
##
## Memory [MB] prior|after|max(diff) : 52.6 | 54.9 | 70.1 (17)
##
## Duration: 0 s
##
## ... PG: raw intensity done
## Starting to work on PG: LFQ intensity ...
##
## Memory [MB] prior|after|max(diff) : 54.9 | 55.6 | 70.1 (15)
##
## Duration: 0 s
##
## ... PG: LFQ intensity done
## Starting to work on PG: Principal Component ...
##
## Memory [MB] prior|after|max(diff) : 55.6 | 56.9 | 96.2 (41)
##
## Duration: 0 s
##
## ... PG: Principal Component done
## Reading file C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/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'!
## Keeping 17 of 62 columns!
## Read 90398 entries from C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/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) : 77.7 | 78.7 | 136 (58)
##
## Duration: 0 s
##
## ... EVD:Contaminant (%s) done
## Starting to work on EVD: Pep Intensity (">%1.1f") ...
##
## Memory [MB] prior|after|max(diff) : 78.7 | 88.6 | 140.9 (62)
##
## Duration: 0 s
##
## ... EVD: Pep Intensity (">%1.1f") done
## Starting to work on EVD: Prot Count (">%1.0f") ...
##
## Memory [MB] prior|after|max(diff) : 89 | 89.1 | 149.8 (61)
##
## Duration: 0 s
##
## ... EVD: Prot Count (">%1.0f") done
## Starting to work on EVD: Pep Count (">%1.0f") ...
##
## Memory [MB] prior|after|max(diff) : 89.1 | 89.2 | 112.5 (23)
##
## Duration: 0 s
##
## ... EVD: Pep Count (">%1.0f") done
## Starting to work on EVD: RT Peak Width ...
##
## Memory [MB] prior|after|max(diff) : 89.2 | 89.5 | 179.6 (90)
##
## Duration: 0 s
##
## ... EVD: RT Peak Width done
## Starting to work on EVD: MBR Align ...
##
## Memory [MB] prior|after|max(diff) : 89.5 | 90.9 | 179.5 (90)
##
## Duration: 5 s
##
## ... EVD: MBR Align done
## Starting to work on EVD: MBR ID-Transfer ...
##
## Memory [MB] prior|after|max(diff) : 90.8 | 91.2 | 292.3 (202)
##
## Duration: 42 s
##
## ... EVD: MBR ID-Transfer done
## Starting to work on EVD: MBR auxilliary ...
##
## Memory [MB] prior|after|max(diff) : 91.2 | 96.7 | 258.1 (167)
##
## Duration: 1 s
##
## ... EVD: MBR auxilliary done
## Starting to work on EVD: Charge ...## Warning: Ignoring unknown aesthetics: width##
## Memory [MB] prior|after|max(diff) : 96.7 | 96.8 | 129.7 (33)
##
## Duration: 0 s
##
## ... EVD: Charge done
## Starting to work on EVD: ID rate over RT ...
##
## Memory [MB] prior|after|max(diff) : 96.8 | 97.1 | 157.5 (61)
##
## 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) : 97.1 | 100.4 | 182.1 (85)
##
## Duration: 0 s
##
## ... EVD: MS Cal-Pre (%1.1f) done
## Starting to work on EVD: MS Cal-Post ...
##
## Memory [MB] prior|after|max(diff) : 100.4 | 103.7 | 181.7 (81)
##
## Duration: 0 s
##
## ... EVD: MS Cal-Post done
## Starting to work on EVD: Contaminants ...
##
## Memory [MB] prior|after|max(diff) : 103.7 | 106.7 | 174.3 (71)
##
## Duration: 0 s
##
## ... EVD: Contaminants done
## Starting to work on EVD: MS^2 Oversampling ...
##
## Memory [MB] prior|after|max(diff) : 106.7 | 106.8 | 155 (48)
##
## Duration: 0 s
##
## ... EVD: MS^2 Oversampling done
## Starting to work on EVD: Pep Missing Values ...
##
## Memory [MB] prior|after|max(diff) : 106.8 | 114.4 | 294.9 (188)
##
## Duration: 1 s
##
## ... EVD: Pep Missing Values done
## Reading file C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/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\RtmpSmzD8i/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) : 210.9 | 214.5 | 290.5 (80)
##
## Duration: 0 s
##
## ... MSMS: MS^2 Cal (%s) done
## Starting to work on MSMS: %s ...
##
## Memory [MB] prior|after|max(diff) : 214.5 | 214.7 | 248.1 (34)
##
## Duration: 0 s
##
## ... MSMS: %s done
## Reading file C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/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\RtmpSmzD8i/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) : 130.4 | 132.2 | 263.9 (134)
##
## Duration: 1 s
##
## ... MS^2*Scans: TopN over RT done
## Starting to work on MS^2*Scans: Ion Inj Time ...
##
## Memory [MB] prior|after|max(diff) : 132.1 | 132.6 | 148.5 (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) : 132.3 | 139.9 | 219.9 (88)
##
## Duration: 0 s
##
## ... MS^2*Scans: Intensity done
## Starting to work on MS^2*Scans: TopN high ...
##
## Memory [MB] prior|after|max(diff) : 139.7 | 139.9 | 156 (16)
##
## 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) : 139.8 | 139.9 | 161.6 (22)
##
## Duration: 0 s
##
## ... MS^2*Scans: TopN ID over N done
## [1] "#Metrics: "
## [1] 32
## Starting to work on Average Overall Quality ...
##
## Memory [MB] prior|after|max(diff) : 139.8 | 139.8 | 140.9 (1)
##
## Duration: 0 s
##
## ... Average Overall Quality done## Warning in FUN(subset, ...): NAs introduced by coercion## Creating Report file ...## 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 pandoc8d0ea23f1f.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\bielow\Documents\R\win-library\3.3\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --number-sections --variable "theme:bootstrap" --include-in-header "C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i\rmarkdown-str8d040117540.html"##
## Output created: C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/txt_20min/report_v0.92.0_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(L_stringMetric, as.graphicsAnnot(x$label)): font
## metrics unknown for character 0xa
## Warning in grid.Call(L_stringMetric, as.graphicsAnnot(x$label)): font
## metrics unknown for character 0xa## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa
## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa## Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa
## Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa
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## $y, : font metrics unknown for character 0xa## Warning: Removed 85 rows containing non-finite values (stat_boxplot).## Warning: position_dodge requires non-overlapping x intervals## Warning in grid.Call(L_stringMetric, as.graphicsAnnot(x$label)): font
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## Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa## Warning: Removed 125 rows containing non-finite values (stat_boxplot).## Warning: position_dodge requires non-overlapping x intervals## Warning in grid.Call(L_stringMetric, as.graphicsAnnot(x$label)): font
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## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
## font metrics unknown for character 0xa## Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa
## Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x
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## Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x
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## Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x
## $y, : font metrics unknown for character 0xa## Warning: Removed 5 rows containing missing values (geom_point).## Warning: Removed 719 rows containing non-finite values (stat_boxplot).## Warning: Removed 779 rows containing non-finite values (stat_boxplot).## Warning: Removed 720 rows containing non-finite values (stat_bin).## Warning: Removed 719 rows containing non-finite values (stat_bin).## done
## Report file created at
##
## C:\Users\bielow\AppData\Local\Temp\RtmpSmzD8i/txt_20min/report_v0.92.0_txt_20min.*
##
##
##
## Time elapsed: 1.6 mincat(paste0("\nReport generated as '", r$report_file, "'\n\n"))##
## Report generated as ''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.