Tutorials/MLMSprocessingTutorial.md
In lilyacb/MLMS: What the Package Does (One Line, Title Case)
title: "RMDdraft1MLMS"
output:
minidown::mini_document:
framework: water
theme: light
code_folding:
source: show
output: show
message: hide
warning: hide
error: show
toc: true
toc_float: true
toc_highlight: true
tabset: true
number_sections: true
anchor_sections: false
self_contained: false
code_download: true
math: "katex"
keep_md: true
fig_caption: true
vignette: >
%\VignetteIndexEntry{Writing Vignette with the 'minidown' Package}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
bibliography: references.bib
This article introduces the MLMS R library and is a draft of a vignette[@R-base].
The github link for MLMS is
github.com/lilyacb/MLMS. Open this document in a browser for the links to work.
Accessing information and making tables
Tables summarizing .dxf file contents can be produced with read_summary().
```{.r .details .show summary='Source'}
datafile<-"170525_NaHCO3 L + NaCl L_.dxf"
#data_file<-"https://github.com/lilyacb/MLMS/blob/main/Data/170525_NaHCO3%2#0L%20%2B%20NaCl%20L_.dxf" # would work if changed to csv!!
#file.summ<-read_csv(data_file)
# Print table without kable
fileI.summ<-read_summary(datafile)
```{.details .show summary='Output'}
## Length Class Mode
## version 1 package_version list
## read_options 4 -none- list
## file_info 16 tbl_df list
## method_info 3 -none- list
## raw_data 5 tbl_df list
## vendor_data_table 39 tbl_df list
You can use kable to make a fancier table.
```{.r .details .show summary='Source'}
#class.source='details hide'
# Using kable
knitr::kable(fileI.summ,caption="170525_NaHCO3 L + NaCl L_.dxf file summary")
<table>
<caption>170525_NaHCO3 L + NaCl L_.dxf file summary</caption>
<thead>
<tr>
<th style="text-align:left;"> </th>
<th style="text-align:left;"> Length </th>
<th style="text-align:left;"> Class </th>
<th style="text-align:left;"> Mode </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> version </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> package_version </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> read_options </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> -none- </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> file_info </td>
<td style="text-align:left;"> 16 </td>
<td style="text-align:left;"> tbl_df </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> method_info </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> -none- </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> raw_data </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> tbl_df </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> vendor_data_table </td>
<td style="text-align:left;"> 39 </td>
<td style="text-align:left;"> tbl_df </td>
<td style="text-align:left;"> list </td>
</tr>
</tbody>
</table>
<br><br>
You can print information contained in the file_info, vendor_info and raw_data tabs of the .dxf file.
Get file information with *file_info()*.
```{.r .details .show summary='Source'}
# Can get file information
fi.df<-file_info(files=datafile)
knitr::kable(fi.df,caption="170525_NaHCO3 L + NaCl L_.dxf file information")
170525_NaHCO3 L + NaCl L_.dxf file information
file_id
Identifier_1
Analysis
Preparation
Date_and_Time
170525_NaHCO3 L + NaCl L_.dxf
NaHCO3 L + NaCl L
4172
2% CO2 in He 24hrs
2017-05-25 21:15:20
Get the vendor data table with vendor_info().
```{.r .details .show summary='Source'}
Can get vendor info
vi.df<-vendor_info(datafile)
kbl(head(vi.df)[1:3,],caption="170525_NaHCO3 L + NaCl L_.dxf vendor data") %>%
kable_paper() %>%
scroll_box(width=5,height = "200px")
<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:200px; overflow-x: scroll; width:5; "><table class=" lightable-paper" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; margin-left: auto; margin-right: auto;'>
<caption>170525_NaHCO3 L + NaCl L_.dxf vendor data</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Identifier_1 </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Peak_Nr </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Start </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Rt </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> End </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Intensity_All </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> rIntensity_All </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Ampl_44 </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Ampl_45 </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Ampl_46 </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> d13C/12C </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> d18O/16O </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NaHCO3 L + NaCl L </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 27.1700000762939 </td>
<td style="text-align:left;"> 47.443000793457 </td>
<td style="text-align:left;"> 50.3689994812012 </td>
<td style="text-align:left;"> 40.90863519699 </td>
<td style="text-align:left;"> 141539.302508887 </td>
<td style="text-align:left;"> 2062.13298836363 </td>
<td style="text-align:left;"> 2371.49813464285 </td>
<td style="text-align:left;"> 2812.49753618504 </td>
<td style="text-align:left;"> -36.8309479493618 </td>
<td style="text-align:left;"> -39.9994709523972 </td>
</tr>
<tr>
<td style="text-align:left;"> NaHCO3 L + NaCl L </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 67.088996887207 </td>
<td style="text-align:left;"> 87.3619995117188 </td>
<td style="text-align:left;"> 90.0790023803711 </td>
<td style="text-align:left;"> 40.8018339597763 </td>
<td style="text-align:left;"> 141166.762952385 </td>
<td style="text-align:left;"> 2065.4354230274 </td>
<td style="text-align:left;"> 2375.34645516822 </td>
<td style="text-align:left;"> 2816.45019646327 </td>
<td style="text-align:left;"> -36.9 </td>
<td style="text-align:left;"> -40.0000000000001 </td>
</tr>
<tr>
<td style="text-align:left;"> NaHCO3 L + NaCl L </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 131.878997802734 </td>
<td style="text-align:left;"> 134.177993774414 </td>
<td style="text-align:left;"> 138.149002075195 </td>
<td style="text-align:left;"> 0.775306018352309 </td>
<td style="text-align:left;"> 2741.90298831581 </td>
<td style="text-align:left;"> 497.765554776576 </td>
<td style="text-align:left;"> 587.296395809005 </td>
<td style="text-align:left;"> 684.745514792838 </td>
<td style="text-align:left;"> -12.8581753517045 </td>
<td style="text-align:left;"> -3.96450973206153 </td>
</tr>
</tbody>
</table></div>
<br>
Get the raw data using *raw_data()*
```{.r .details .show summary='Source'}
# Can get the raw data
raw.df<-raw_data(datafile)
knitr::kable(head(raw.df),caption="170525_NaHCO3 L + NaCl L_.dxf raw data")
170525_NaHCO3 L + NaCl L_.dxf raw data
file_id
tp
time.s
v44.mV
v45.mV
v46.mV
170525_NaHCO3 L + NaCl L_.dxf
1
0.209
1.412726
0.8119730
2.852197
170525_NaHCO3 L + NaCl L_.dxf
2
0.418
1.416549
0.8024275
2.854114
170525_NaHCO3 L + NaCl L_.dxf
3
0.627
1.414637
0.7928824
2.823437
170525_NaHCO3 L + NaCl L_.dxf
4
0.836
1.412726
0.9628401
3.186850
170525_NaHCO3 L + NaCl L_.dxf
5
1.045
1.406990
0.8768920
3.003719
170525_NaHCO3 L + NaCl L_.dxf
6
1.254
1.410814
0.7508881
2.712264
Get the resistor information using resistor_data()
```{.r .details .show summary='Source'}
Can get the resistor information
resist<-resistor_data(datafile)
knitr::kable(resist,caption="170525_NaHCO3 L + NaCl L_.dxf resistor information")
<table>
<caption>170525_NaHCO3 L + NaCl L_.dxf resistor information</caption>
<thead>
<tr>
<th style="text-align:left;"> file_id </th>
<th style="text-align:right;"> cup </th>
<th style="text-align:right;"> R.Ohm </th>
<th style="text-align:left;"> mass </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> 170525_NaHCO3 L + NaCl L_.dxf </td>
<td style="text-align:right;"> 1 </td>
<td style="text-align:right;"> 3e+08 </td>
<td style="text-align:left;"> 44 </td>
</tr>
<tr>
<td style="text-align:left;"> 170525_NaHCO3 L + NaCl L_.dxf </td>
<td style="text-align:right;"> 2 </td>
<td style="text-align:right;"> 3e+10 </td>
<td style="text-align:left;"> 45 </td>
</tr>
<tr>
<td style="text-align:left;"> 170525_NaHCO3 L + NaCl L_.dxf </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 1e+11 </td>
<td style="text-align:left;"> 46 </td>
</tr>
</tbody>
</table>
<br>
Get the isotopic reference values with *reference_values_ratio()*
```{.r .details .show summary='Source'}
# Can get isotopic reference values with ratios
stand_ratio<-reference_values_ratio(datafile)
knitr::kable(stand_ratio,caption="170525_NaHCO3 L + NaCl L_.dxf isotopic reference values with ratios")
170525_NaHCO3 L + NaCl L_.dxf isotopic reference values with ratios
file_id
standard
gas
delta_name
delta_value
reference
element
ratio_name
ratio_value
170525_NaHCO3 L + NaCl L_.dxf
CO2_zero
CO2
d 13C/12C
-36.9
VPDB
C
R 13C/12C
0.0111802
170525_NaHCO3 L + NaCl L_.dxf
CO2_zero
CO2
d 13C/12C
-36.9
VPDB
O
R 18O/16O
0.0020672
170525_NaHCO3 L + NaCl L_.dxf
CO2_zero
CO2
d 13C/12C
-36.9
VPDB
O
R 17O/16O
0.0003860
170525_NaHCO3 L + NaCl L_.dxf
CO2_zero
CO2
d 18O/16O
-40.0
VSMOW
H
R 2H/1H
0.0001558
170525_NaHCO3 L + NaCl L_.dxf
CO2_zero
CO2
d 18O/16O
-40.0
VSMOW
O
R 17O/16O
0.0003799
170525_NaHCO3 L + NaCl L_.dxf
CO2_zero
CO2
d 18O/16O
-40.0
VSMOW
O
R 18O/16O
0.0020052
Use DT to render larger tables neatly. You can show only a few lines, have a search bar, filters and more.
```{.r .details .show summary='Source'}
datatable(vi.df,#filter="top",
options=list(pageLength=5,scrollX=T))
```{=html}
<div id="htmlwidget-16cf68eae5f8a8f2b275" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-16cf68eae5f8a8f2b275">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16"],["NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L","NaHCO3 L + NaCl L"],["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16"],["27.1700000762939","67.088996887207","131.878997802734","166.572998046875","206.492004394531","271.282012939453","331.055999755859","390.621002197266","450.394989013672","510.169006347656","569.942993164062","629.716979980469","689.281982421875","749.056030273438","808.620971679688","843.315002441406"],["47.443000793457","87.3619995117188","134.177993774414","186.845993041992","226.555999755859","275.252990722656","334.817993164062","394.592010498047","454.365997314453","513.931030273438","573.705017089844","633.47900390625","693.252990722656","752.817993164062","812.591979980469","863.588012695312"],["50.3689994812012","90.0790023803711","138.149002075195","189.563003540039","229.481994628906","281.523010253906","341.088012695312","400.861999511719","460.427001953125","520.200988769531","579.765991210938","639.539978027344","699.10498046875","758.879028320312","818.443969726562","866.513977050781"],["40.90863519699","40.8018339597763","0.775306018352309","40.7667643372804","40.5869572281707","3.2905863791484","3.13872566031333","2.99676108613764","2.86171429394237","2.73679153407845","2.62090716786112","2.51637866908364","2.41483946341397","2.31754065522929","2.22933039823088","40.7124472200286"],["141539.302508887","141166.762952385","2741.90298831581","141046.972056521","140423.818600922","11634.7360679161","11097.4910169777","10595.5253245978","10116.641868754","9675.86233312315","9264.64028335832","8894.88525895595","8536.21830667717","8190.25073574662","7878.85016825028","140862.365302356"],["2062.13298836363","2065.4354230274","497.765554776576","2065.33132567091","2065.95164329982","835.629396537048","796.707468988884","760.583045951027","727.136230359232","695.731342346527","666.690982593185","639.816551703906","614.178994448332","590.535712752739","568.269862700224","2059.70138770054"],["2371.49813464285","2375.34645516822","587.296395809005","2375.28129849837","2375.8375421133","983.807398920264","938.38670479377","895.553766797341","855.914217894725","819.130433390809","784.737002483931","753.050001131472","722.521469497472","694.496962038834","668.386176906104","2368.64119184778"],["2812.49753618504","2816.45019646327","684.745514792838","2815.76340254216","2816.62504109653","1181.01548866047","1126.1267886412","1074.98412818962","1027.52041625678","983.555646869736","941.803287231497","904.883046181393","868.365553263493","833.933201559691","803.193882381927","2808.72003462978"],["-36.8309479493618","-36.9","-12.8581753517045","-36.8501122637148","-36.8704263734039","-13.3314973496644","-13.4239050632513","-13.6527361443061","-13.7448311807784","-13.798912139493","-13.889804179784","-14.0983142851769","-14.2407335597668","-14.5823805444807","-14.4921650499025","-36.817546278087"],["-39.9994709523972","-40.0000000000001","-3.96450973206153","-40.0105813222899","-40.0135757068457","-4.15988057764383","-4.15856399628201","-3.99410487962526","-4.27067517196855","-4.01350290214231","-4.3526332497722","-4.26916577111913","-4.08914826967777","-4.44953861274611","-4.4104799888387","-39.9775032876957"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>Identifier_1<\/th>\n <th>Peak_Nr<\/th>\n <th>Start<\/th>\n <th>Rt<\/th>\n <th>End<\/th>\n <th>Intensity_All<\/th>\n <th>rIntensity_All<\/th>\n <th>Ampl_44<\/th>\n <th>Ampl_45<\/th>\n <th>Ampl_46<\/th>\n <th>d13C/12C<\/th>\n <th>d18O/16O<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"pageLength":5,"scrollX":true,"order":[],"autoWidth":false,"orderClasses":false,"columnDefs":[{"orderable":false,"targets":0}],"lengthMenu":[5,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>
MS data processing
Peak areas
Peak areas were calculated using the trapz package, which implements numerical integration via the trapezoid rule.
Math with KaTex produces nice equations. You can highlight formulas or text.
The trapezoid rule:
div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;}
$$
\int\limits_a^b f(x)dx\approx
\sum_{n=0}^{N-1}{\frac{1}{2}(f_n+f_{n+1})(\varDelta x)_n}
$$
You can insert images into an RMD doc.
```{.r .details .show summary='Source'}
trapImg<-readPNG("trapezoidalRuleImg.png")
grid.raster(trapImg)
<br>
Calculate the peak areas using *trap_area_allPks()*.
```{.r .details .show summary='Source'}
# Can get peak areas
rawN<-"v44.mV"
areaPks<-trap_area_allPks(raw.df,vi.df,rawN)
knitr::kable(areaPks,caption="170525_NaHCO3 L + NaCl L_.dxf all peak areas")
170525_NaHCO3 L + NaCl L_.dxf all peak areas
Pk_Nr
trap_area
1
40.6839545
2
40.5842293
3
0.7984758
4
40.5428463
5
40.3672183
6
3.3203306
7
3.1683712
8
3.0249778
9
2.8898409
10
2.7635269
11
2.6484939
12
2.5426593
13
2.4407975
14
2.3417151
15
2.2528789
16
40.4814526
Data visualization
p.caption {
font-size: 0.9em;
font-style: italic;
color: grey;
margin-right: 10%;
margin-left: 10%;<br />
text-align: justify;
}
You can graph the intensity vs retention time using plot_ms().
```{.r .details .show summary='Source'}
Intensity_All vs Rt for an experiment
ia.xname<-"Rt"
ia.yname<-"Intensity_All"
plot
plot_ms(vi.df,ia.xname,ia.yname)
<br><br>
Plot individual peaks in an experiment with *plot_individual_peaks()*.
```{.r .details .show summary='Source'}
# Can plot peaks in an experiment individually (Intensity (mV) vs Rt)
time.s<-as.numeric(raw.df$time.s)
start.v1<-as.numeric(vi.df$Start)
end.v1<-as.numeric(vi.df$End)
v44<-as.numeric(raw.df$v44.mV)
# plot just the first peak to inspect
peak1.p<-plot_individual_peaks(start.v1,end.v1,time.s,v44,"1","v44.mV")
Plot the raw data, intensity vs retention time, with gg_raw_plot()--make function!!
Use ggplot to plot the raw (redo colour label in legend)
```{.r .details .show summary='Source'}
raw.dat<-read.table("LLrawdat")
ggplot(raw.dat,aes(x=time.s,y=v44.mV))+
geom_line(aes(color="v44.mV"))+
geom_line(aes(x=time.s,y=v45.mV,color="v45.mV"))+
geom_line(aes(x=time.s,y=v46.mV,color="v46.mV"))+
labs(title="170525_NaHCO3 L + NaCl U",x="time.s",y="v44_v45_v46.mV")
<!-- -->
<br>
Plot the raw data of all files in a directory and export to a pdf file using *generic_plot_all_raw()* **change to ggplot version**--new func!
```{.r .details .show summary='Source'}
# Can plot raw data of all files in a directory
# Get all filenames of .dxf files in the directory
LLdir<-"NaHCO3_L_+_NaCl_L"
fileNames<-all_filenames(LLdir)
setwd(LLdir)
rawList<-raw_data_all(fileNames)
setwd("~/Desktop/EuropaMLMS/rmdMLMS")
# plot all raw data
generic_plot_all_raw(rawList)
Sorting and quality checks
Automated sorting of a directory of .dxf files
A directory of .dxf files can be organized by Identifier_1 and Preparation method.
Contents of an unsorted directory of .dxf files.
```{.details .show summary='Output'}
[1] "170525_NaHCO3 L + NaCl L_.dxf" "170525_NaHCO3 L + NaCl U_.dxf"
[3] "170525_NaHCO3 L_.dxf" "170525_NaHCO3 U + NaCl L_.dxf"
[5] "170525_NaHCO3 U + NaCl U_.dxf" "170525_NaHCO3 U_.dxf"
<br>
Use *sort_by_identifier_1()* to sort a directory of .dxf files by Identifier_1
```{.r .details .show summary='Source'}
# Use Identifier_1 labels to sort data
unsortedPath<-"~/Desktop/EuropaMLMS/rmdMLMS/vignetteData/sortFolder"
setwd(unsortedPath)
sort_by_identifier_1(unsortedPath)
setwd("~/Desktop/EuropaMLMS/rmdMLMS")
Contents of the sorted directory.
```{.details .show summary='Output'}
[1] "cache" "NaHCO3 L" "NaHCO3 L + NaCl L"
[4] "NaHCO3 L + NaCl U" "NaHCO3 U" "NaHCO3 U + NaCl L"
[7] "NaHCO3 U + NaCl U"
<br>
### Automated quality-control and calibration of a directory of .dxf files
Perform quality checks and remove files that fail any of the checks.
<body>
**Quality checks:**
<ul>
1.
2.
3.
4.
5.
6.
</ul>
<body>
The list above represents the order of quality checks and a file is removed immediately after it fails a check (before the next check is performed).
**1. Peaks present/number of peaks **<br>
Check that there are more than 0 and fewer than a specified number of peaks.
**2. Reference peaks**<br>
Check-
**3. Reference peaks**<br>
checks-
<br>
#### Quality-control summary for a directory of .dxf files {.tabset .tabset-fade .tabset-pills}
Output from the quality check and calibration process can summarized in tables and analyzed.
##### QC1 {.unnumbered}
(tab content)
##### QC2 {.unnumbered}
(tab content)
#### {.unnumbered}
Summaries for analyses that failed checks
<br><br>
#### Internal standards summary for a directory of .dxf files (if standards present)
Internal standards can be checked for a batch of runs (several .dxf files with internal standard experiments).
<br><br>
### Automated separation and quality-control of reference and sample peaks in a combined .csv file for multiple experiments
Processing of weekeqdata (three .csv files) into quality-checked reference and sample peaks
<br><br>
# UMAP
Illustration of interactive graphics
## Unfiltered data
UMAP for different reactions that have not been quality-checked.<br>
This UMAP uses a directory of unsorted, unfiltered data and is for all the peaks in the data set.
```{.r .details .show summary='Source'}
unfiltPlot.dat<-read.table("UMAP_NaHCO3_+_NaCl_notQC")
p<-ggplot(unfiltPlot.dat,
aes(x=x,y=y,color=Identifier_1))+
geom_point()+
labs(title="UMAP of NaHCO3 + NaCl (not quality-checked)")
ggplotly(p)
```{=html}
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<br><br>
## Quality-controlled data
UMAP for different reactions that have been quality-checked.<br>
EXAMPLE of interactive plot with multiple variables (NOT MLMS data)
```{.r .details .show summary='Source'}
library(gapminder)
p <- gapminder %>%
filter(year==1977) %>%
ggplot( aes(gdpPercap, lifeExp, size = pop, color=continent)) +
geom_point() +
scale_x_log10() +
theme_bw()
ggplotly(p)
{=html}
<div id="htmlwidget-d4ce28c285f7f8ecc7e7" style="width:672px;height:480px;" class="plotly html-widget"></div>
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References
lilyacb/MLMS documentation built on July 21, 2023, 4:12 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
title: "RMDdraft1MLMS" output: minidown::mini_document: framework: water theme: light code_folding: source: show output: show message: hide warning: hide error: show toc: true toc_float: true toc_highlight: true tabset: true number_sections: true anchor_sections: false self_contained: false code_download: true math: "katex" keep_md: true fig_caption: true vignette: > %\VignetteIndexEntry{Writing Vignette with the 'minidown' Package} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} bibliography: references.bib
This article introduces the MLMS R library and is a draft of a vignette[@R-base].
The github link for MLMS is github.com/lilyacb/MLMS. Open this document in a browser for the links to work.
Accessing information and making tables
Tables summarizing .dxf file contents can be produced with read_summary().
```{.r .details .show summary='Source'} datafile<-"170525_NaHCO3 L + NaCl L_.dxf" #data_file<-"https://github.com/lilyacb/MLMS/blob/main/Data/170525_NaHCO3%2#0L%20%2B%20NaCl%20L_.dxf" # would work if changed to csv!! #file.summ<-read_csv(data_file) # Print table without kable fileI.summ<-read_summary(datafile)
```{.details .show summary='Output'}
## Length Class Mode
## version 1 package_version list
## read_options 4 -none- list
## file_info 16 tbl_df list
## method_info 3 -none- list
## raw_data 5 tbl_df list
## vendor_data_table 39 tbl_df list
You can use kable to make a fancier table.
```{.r .details .show summary='Source'} #class.source='details hide' # Using kable knitr::kable(fileI.summ,caption="170525_NaHCO3 L + NaCl L_.dxf file summary")
<table>
<caption>170525_NaHCO3 L + NaCl L_.dxf file summary</caption>
<thead>
<tr>
<th style="text-align:left;"> </th>
<th style="text-align:left;"> Length </th>
<th style="text-align:left;"> Class </th>
<th style="text-align:left;"> Mode </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> version </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> package_version </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> read_options </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> -none- </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> file_info </td>
<td style="text-align:left;"> 16 </td>
<td style="text-align:left;"> tbl_df </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> method_info </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> -none- </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> raw_data </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> tbl_df </td>
<td style="text-align:left;"> list </td>
</tr>
<tr>
<td style="text-align:left;"> vendor_data_table </td>
<td style="text-align:left;"> 39 </td>
<td style="text-align:left;"> tbl_df </td>
<td style="text-align:left;"> list </td>
</tr>
</tbody>
</table>
<br><br>
You can print information contained in the file_info, vendor_info and raw_data tabs of the .dxf file.
Get file information with *file_info()*.
```{.r .details .show summary='Source'}
# Can get file information
fi.df<-file_info(files=datafile)
knitr::kable(fi.df,caption="170525_NaHCO3 L + NaCl L_.dxf file information")
Get the vendor data table with vendor_info().
```{.r .details .show summary='Source'}
Can get vendor info
vi.df<-vendor_info(datafile) kbl(head(vi.df)[1:3,],caption="170525_NaHCO3 L + NaCl L_.dxf vendor data") %>% kable_paper() %>% scroll_box(width=5,height = "200px")
<div style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:200px; overflow-x: scroll; width:5; "><table class=" lightable-paper" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; margin-left: auto; margin-right: auto;'>
<caption>170525_NaHCO3 L + NaCl L_.dxf vendor data</caption>
<thead>
<tr>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Identifier_1 </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Peak_Nr </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Start </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Rt </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> End </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Intensity_All </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> rIntensity_All </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Ampl_44 </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Ampl_45 </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Ampl_46 </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> d13C/12C </th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> d18O/16O </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> NaHCO3 L + NaCl L </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 27.1700000762939 </td>
<td style="text-align:left;"> 47.443000793457 </td>
<td style="text-align:left;"> 50.3689994812012 </td>
<td style="text-align:left;"> 40.90863519699 </td>
<td style="text-align:left;"> 141539.302508887 </td>
<td style="text-align:left;"> 2062.13298836363 </td>
<td style="text-align:left;"> 2371.49813464285 </td>
<td style="text-align:left;"> 2812.49753618504 </td>
<td style="text-align:left;"> -36.8309479493618 </td>
<td style="text-align:left;"> -39.9994709523972 </td>
</tr>
<tr>
<td style="text-align:left;"> NaHCO3 L + NaCl L </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 67.088996887207 </td>
<td style="text-align:left;"> 87.3619995117188 </td>
<td style="text-align:left;"> 90.0790023803711 </td>
<td style="text-align:left;"> 40.8018339597763 </td>
<td style="text-align:left;"> 141166.762952385 </td>
<td style="text-align:left;"> 2065.4354230274 </td>
<td style="text-align:left;"> 2375.34645516822 </td>
<td style="text-align:left;"> 2816.45019646327 </td>
<td style="text-align:left;"> -36.9 </td>
<td style="text-align:left;"> -40.0000000000001 </td>
</tr>
<tr>
<td style="text-align:left;"> NaHCO3 L + NaCl L </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 131.878997802734 </td>
<td style="text-align:left;"> 134.177993774414 </td>
<td style="text-align:left;"> 138.149002075195 </td>
<td style="text-align:left;"> 0.775306018352309 </td>
<td style="text-align:left;"> 2741.90298831581 </td>
<td style="text-align:left;"> 497.765554776576 </td>
<td style="text-align:left;"> 587.296395809005 </td>
<td style="text-align:left;"> 684.745514792838 </td>
<td style="text-align:left;"> -12.8581753517045 </td>
<td style="text-align:left;"> -3.96450973206153 </td>
</tr>
</tbody>
</table></div>
<br>
Get the raw data using *raw_data()*
```{.r .details .show summary='Source'}
# Can get the raw data
raw.df<-raw_data(datafile)
knitr::kable(head(raw.df),caption="170525_NaHCO3 L + NaCl L_.dxf raw data")
Get the resistor information using resistor_data()
```{.r .details .show summary='Source'}
Can get the resistor information
resist<-resistor_data(datafile) knitr::kable(resist,caption="170525_NaHCO3 L + NaCl L_.dxf resistor information")
<table>
<caption>170525_NaHCO3 L + NaCl L_.dxf resistor information</caption>
<thead>
<tr>
<th style="text-align:left;"> file_id </th>
<th style="text-align:right;"> cup </th>
<th style="text-align:right;"> R.Ohm </th>
<th style="text-align:left;"> mass </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;"> 170525_NaHCO3 L + NaCl L_.dxf </td>
<td style="text-align:right;"> 1 </td>
<td style="text-align:right;"> 3e+08 </td>
<td style="text-align:left;"> 44 </td>
</tr>
<tr>
<td style="text-align:left;"> 170525_NaHCO3 L + NaCl L_.dxf </td>
<td style="text-align:right;"> 2 </td>
<td style="text-align:right;"> 3e+10 </td>
<td style="text-align:left;"> 45 </td>
</tr>
<tr>
<td style="text-align:left;"> 170525_NaHCO3 L + NaCl L_.dxf </td>
<td style="text-align:right;"> 3 </td>
<td style="text-align:right;"> 1e+11 </td>
<td style="text-align:left;"> 46 </td>
</tr>
</tbody>
</table>
<br>
Get the isotopic reference values with *reference_values_ratio()*
```{.r .details .show summary='Source'}
# Can get isotopic reference values with ratios
stand_ratio<-reference_values_ratio(datafile)
knitr::kable(stand_ratio,caption="170525_NaHCO3 L + NaCl L_.dxf isotopic reference values with ratios")
Use DT to render larger tables neatly. You can show only a few lines, have a search bar, filters and more.
```{.r .details .show summary='Source'} datatable(vi.df,#filter="top", options=list(pageLength=5,scrollX=T))
```{=html}
<div id="htmlwidget-16cf68eae5f8a8f2b275" style="width:100%;height:auto;" class="datatables html-widget"></div>
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MS data processing
Peak areas
Peak areas were calculated using the trapz package, which implements numerical integration via the trapezoid rule.
Math with KaTex produces nice equations. You can highlight formulas or text. The trapezoid rule: div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;}
$$
\int\limits_a^b f(x)dx\approx
\sum_{n=0}^{N-1}{\frac{1}{2}(f_n+f_{n+1})(\varDelta x)_n}
$$
You can insert images into an RMD doc.
```{.r .details .show summary='Source'} trapImg<-readPNG("trapezoidalRuleImg.png") grid.raster(trapImg)
<br>
Calculate the peak areas using *trap_area_allPks()*.
```{.r .details .show summary='Source'}
# Can get peak areas
rawN<-"v44.mV"
areaPks<-trap_area_allPks(raw.df,vi.df,rawN)
knitr::kable(areaPks,caption="170525_NaHCO3 L + NaCl L_.dxf all peak areas")
Data visualization
p.caption { font-size: 0.9em; font-style: italic; color: grey; margin-right: 10%; margin-left: 10%;<br /> text-align: justify; }
You can graph the intensity vs retention time using plot_ms().
```{.r .details .show summary='Source'}
Intensity_All vs Rt for an experiment
ia.xname<-"Rt" ia.yname<-"Intensity_All"
plot
plot_ms(vi.df,ia.xname,ia.yname)
<br><br>
Plot individual peaks in an experiment with *plot_individual_peaks()*.
```{.r .details .show summary='Source'}
# Can plot peaks in an experiment individually (Intensity (mV) vs Rt)
time.s<-as.numeric(raw.df$time.s)
start.v1<-as.numeric(vi.df$Start)
end.v1<-as.numeric(vi.df$End)
v44<-as.numeric(raw.df$v44.mV)
# plot just the first peak to inspect
peak1.p<-plot_individual_peaks(start.v1,end.v1,time.s,v44,"1","v44.mV")
Plot the raw data, intensity vs retention time, with gg_raw_plot()--make function!!
Use ggplot to plot the raw (redo colour label in legend)
```{.r .details .show summary='Source'} raw.dat<-read.table("LLrawdat") ggplot(raw.dat,aes(x=time.s,y=v44.mV))+ geom_line(aes(color="v44.mV"))+ geom_line(aes(x=time.s,y=v45.mV,color="v45.mV"))+ geom_line(aes(x=time.s,y=v46.mV,color="v46.mV"))+ labs(title="170525_NaHCO3 L + NaCl U",x="time.s",y="v44_v45_v46.mV")
<!-- -->
<br>
Plot the raw data of all files in a directory and export to a pdf file using *generic_plot_all_raw()* **change to ggplot version**--new func!
```{.r .details .show summary='Source'}
# Can plot raw data of all files in a directory
# Get all filenames of .dxf files in the directory
LLdir<-"NaHCO3_L_+_NaCl_L"
fileNames<-all_filenames(LLdir)
setwd(LLdir)
rawList<-raw_data_all(fileNames)
setwd("~/Desktop/EuropaMLMS/rmdMLMS")
# plot all raw data
generic_plot_all_raw(rawList)
Sorting and quality checks
Automated sorting of a directory of .dxf files
A directory of .dxf files can be organized by Identifier_1 and Preparation method.
Contents of an unsorted directory of .dxf files.
```{.details .show summary='Output'}
[1] "170525_NaHCO3 L + NaCl L_.dxf" "170525_NaHCO3 L + NaCl U_.dxf"
[3] "170525_NaHCO3 L_.dxf" "170525_NaHCO3 U + NaCl L_.dxf"
[5] "170525_NaHCO3 U + NaCl U_.dxf" "170525_NaHCO3 U_.dxf"
<br>
Use *sort_by_identifier_1()* to sort a directory of .dxf files by Identifier_1
```{.r .details .show summary='Source'}
# Use Identifier_1 labels to sort data
unsortedPath<-"~/Desktop/EuropaMLMS/rmdMLMS/vignetteData/sortFolder"
setwd(unsortedPath)
sort_by_identifier_1(unsortedPath)
setwd("~/Desktop/EuropaMLMS/rmdMLMS")
Contents of the sorted directory.
```{.details .show summary='Output'}
[1] "cache" "NaHCO3 L" "NaHCO3 L + NaCl L"
[4] "NaHCO3 L + NaCl U" "NaHCO3 U" "NaHCO3 U + NaCl L"
[7] "NaHCO3 U + NaCl U"
<br>
### Automated quality-control and calibration of a directory of .dxf files
Perform quality checks and remove files that fail any of the checks.
<body>
**Quality checks:**
<ul>
1.
2.
3.
4.
5.
6.
</ul>
<body>
The list above represents the order of quality checks and a file is removed immediately after it fails a check (before the next check is performed).
**1. Peaks present/number of peaks **<br>
Check that there are more than 0 and fewer than a specified number of peaks.
**2. Reference peaks**<br>
Check-
**3. Reference peaks**<br>
checks-
<br>
#### Quality-control summary for a directory of .dxf files {.tabset .tabset-fade .tabset-pills}
Output from the quality check and calibration process can summarized in tables and analyzed.
##### QC1 {.unnumbered}
(tab content)
##### QC2 {.unnumbered}
(tab content)
#### {.unnumbered}
Summaries for analyses that failed checks
<br><br>
#### Internal standards summary for a directory of .dxf files (if standards present)
Internal standards can be checked for a batch of runs (several .dxf files with internal standard experiments).
<br><br>
### Automated separation and quality-control of reference and sample peaks in a combined .csv file for multiple experiments
Processing of weekeqdata (three .csv files) into quality-checked reference and sample peaks
<br><br>
# UMAP
Illustration of interactive graphics
## Unfiltered data
UMAP for different reactions that have not been quality-checked.<br>
This UMAP uses a directory of unsorted, unfiltered data and is for all the peaks in the data set.
```{.r .details .show summary='Source'}
unfiltPlot.dat<-read.table("UMAP_NaHCO3_+_NaCl_notQC")
p<-ggplot(unfiltPlot.dat,
aes(x=x,y=y,color=Identifier_1))+
geom_point()+
labs(title="UMAP of NaHCO3 + NaCl (not quality-checked)")
ggplotly(p)
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<br><br>
## Quality-controlled data
UMAP for different reactions that have been quality-checked.<br>
EXAMPLE of interactive plot with multiple variables (NOT MLMS data)
```{.r .details .show summary='Source'}
library(gapminder)
p <- gapminder %>%
filter(year==1977) %>%
ggplot( aes(gdpPercap, lifeExp, size = pop, color=continent)) +
geom_point() +
scale_x_log10() +
theme_bw()
ggplotly(p)
{=html}
<div id="htmlwidget-d4ce28c285f7f8ecc7e7" style="width:672px;height:480px;" class="plotly html-widget"></div>
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