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diff --git a/figures/AffinityDesigner/fig_S02_synthesis.afdesign b/figures/AffinityDesigner/fig_S02_synthesis.afdesign new file mode 100644 index 0000000..1f4baee Binary files /dev/null and b/figures/AffinityDesigner/fig_S02_synthesis.afdesign differ diff --git a/pdf/S02f.pdf b/pdf/S02f.pdf index d31c48c..c67308c 100644 Binary files a/pdf/S02f.pdf and b/pdf/S02f.pdf differ diff --git a/pdf/fig_S02_synthesis.pdf b/pdf/fig_S02_synthesis.pdf index a0e47a2..d101b5f 100644 Binary files a/pdf/fig_S02_synthesis.pdf and b/pdf/fig_S02_synthesis.pdf differ diff --git a/supplementary_fig02.md b/supplementary_fig02.md index d38342e..06c691f 100644 --- a/supplementary_fig02.md +++ b/supplementary_fig02.md @@ -1,5 +1,17 @@ # supplementary_fig02 -Daniel Fürth +Daniel Fürth

Table of Contents: + +- [Create a table of raw data files](#create-a-table-of-raw-data-files) +- [Import the data](#import-the-data) +- [Make a master data frame with all + data.](#make-a-master-data-frame-with-all-data.) +- [Make a plot](#make-a-plot) +- [Same for MS data](#same-for-ms-data) + - [Peak-detection and annotation in + MS](#peak-detection-and-annotation-in-ms) +- [Bargraph of TFP-ester labeling + gels](#bargraph-of-tfp-ester-labeling-gels) +- [Absorption spectrum](#absorption-spectrum) ## Create a table of raw data files @@ -504,6 +516,57 @@ ms.plot(msdata[msdata$sample=='Azido',]) ![](supplementary_fig02_files/figure-commonmark/unnamed-chunk-21-1.png) +Nice. Now we also need to add peak-detection to it. We will use the +package +[MassSpecWavelet](https://rdrr.io/bioc/MassSpecWavelet/man/MassSpecWavelet.package.html). + +## Peak-detection and annotation in MS + +``` r +#check if devtools is installed. It is used to +if(!require(devtools)){ + install.packages('devtools') +} +``` + + Loading required package: devtools + + Loading required package: usethis + +``` r +library(devtools) + +#check if MassSpecWavelet is installed, it is used to call peaks in MS data. +if(!require(MassSpecWavelet)){ + devtools::install_github('https://github.com/zeehio/MassSpecWavelet') +} +``` + + Loading required package: MassSpecWavelet + +``` r +library(MassSpecWavelet) + +peakInfo <- peakDetectionCWT(msdata[msdata$sample=='Azido',]$intensity, SNR.Th=3) +majorPeakInfo <- peakInfo$majorPeakInfo +peakIndex <- majorPeakInfo$peakIndex + + +ms.plot(msdata[msdata$sample=='Azido',]) + +xpos <-msdata[msdata$sample=='Azido',]$mass.mz[peakIndex] +ypos <- msdata[msdata$sample=='Azido',]$intensity.perc[peakIndex] + +points(xpos, ypos, col='red', pch=21, xpd=TRUE) + +#pos=3 will print the label above the point, 1 = under, 2 = left, 4 = right. +text(xpos, ypos, round(xpos,2), pos=3, xpd=TRUE) +``` + +![](supplementary_fig02_files/figure-commonmark/unnamed-chunk-22-1.png) + +S lets add this to out function: + Then lets plot all the samples on one row each: ``` r @@ -514,7 +577,7 @@ for(i in seq_along(msSamples) ){ } ``` -![](supplementary_fig02_files/figure-commonmark/unnamed-chunk-22-1.png) +![](supplementary_fig02_files/figure-commonmark/unnamed-chunk-24-1.png) Plot a figure: @@ -536,7 +599,7 @@ ms.plot(msdata[msdata$sample == 'RXN594',], col = RColorBrewer::brewer.pal(6, 'P text(1300, 90, mylabels[1], col = RColorBrewer::brewer.pal(6, 'PuOr')[6]) ``` -![](supplementary_fig02_files/figure-commonmark/unnamed-chunk-23-1.png) +![](supplementary_fig02_files/figure-commonmark/unnamed-chunk-25-1.png) Lets save the figure as a PDF: @@ -566,7 +629,7 @@ text(mean(bar[-1]), -1.1, 'Goat-PEG4-TCO\nAZdye488-bis(PEG2-Tz)', xpd=TRUE) lines(c(bar[2]-.25, bar[4]+.25), rep(-0.75, 2), xpd = TRUE) ``` -![](supplementary_fig02_files/figure-commonmark/unnamed-chunk-25-1.png) +![](supplementary_fig02_files/figure-commonmark/unnamed-chunk-27-1.png) Save as PDF: @@ -576,3 +639,5 @@ quartz.save(file='./pdf/S02f.pdf', type='pdf') quartz_off_screen 2 + +# Absorption spectrum diff --git a/supplementary_fig02.qmd b/supplementary_fig02.qmd index e2e44f8..d11d11f 100644 --- a/supplementary_fig02.qmd +++ b/supplementary_fig02.qmd @@ -1,7 +1,8 @@ --- title: "supplementary_fig02" -author: "Daniel Fürth" +author: "Daniel Fürth

Table of Contents:" format: gfm +toc: true --- ## Create a table of raw data files @@ -296,6 +297,44 @@ Lets try it: ```{r} ms.plot(msdata[msdata$sample=='Azido',]) ``` +Nice. Now we also need to add peak-detection to it. We will use the package [MassSpecWavelet](https://rdrr.io/bioc/MassSpecWavelet/man/MassSpecWavelet.package.html). + +## Peak-detection and annotation in MS + +```{r} +#check if devtools is installed. It is used to +if(!require(devtools)){ + install.packages('devtools') +} +library(devtools) + +#check if MassSpecWavelet is installed, it is used to call peaks in MS data. +if(!require(MassSpecWavelet)){ + devtools::install_github('https://github.com/zeehio/MassSpecWavelet') +} +library(MassSpecWavelet) + +peakInfo <- peakDetectionCWT(msdata[msdata$sample=='Azido',]$intensity, SNR.Th=3) +majorPeakInfo <- peakInfo$majorPeakInfo +peakIndex <- majorPeakInfo$peakIndex + + +ms.plot(msdata[msdata$sample=='Azido',]) + +xpos <-msdata[msdata$sample=='Azido',]$mass.mz[peakIndex] +ypos <- msdata[msdata$sample=='Azido',]$intensity.perc[peakIndex] + +points(xpos, ypos, col='red', pch=21, xpd=TRUE) + +#pos=3 will print the label above the point, 1 = under, 2 = left, 4 = right. +text(xpos, ypos, round(xpos,2), pos=3, xpd=TRUE) +``` + +S lets add this to out function: + +```{r} +``` + Then lets plot all the samples on one row each: ```{r} @@ -355,3 +394,6 @@ Save as PDF: ```{r} quartz.save(file='./pdf/S02f.pdf', type='pdf') ``` + +# Absorption spectrum + diff --git a/supplementary_fig02_files/figure-commonmark/unnamed-chunk-22-1.png b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-22-1.png index 88395bb..d48dd28 100644 Binary files a/supplementary_fig02_files/figure-commonmark/unnamed-chunk-22-1.png and b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-22-1.png differ diff --git a/supplementary_fig02_files/figure-commonmark/unnamed-chunk-23-1.png b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-23-1.png index e45b48c..88395bb 100644 Binary files a/supplementary_fig02_files/figure-commonmark/unnamed-chunk-23-1.png and b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-23-1.png differ diff --git a/supplementary_fig02_files/figure-commonmark/unnamed-chunk-24-1.png b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-24-1.png new file mode 100644 index 0000000..88395bb Binary files /dev/null and b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-24-1.png differ diff --git a/supplementary_fig02_files/figure-commonmark/unnamed-chunk-25-1.png b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-25-1.png index 87d40f8..e45b48c 100644 Binary files a/supplementary_fig02_files/figure-commonmark/unnamed-chunk-25-1.png and b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-25-1.png differ diff --git a/supplementary_fig02_files/figure-commonmark/unnamed-chunk-26-1.png b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-26-1.png new file mode 100644 index 0000000..87d40f8 Binary files /dev/null and b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-26-1.png differ diff --git a/supplementary_fig02_files/figure-commonmark/unnamed-chunk-27-1.png b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-27-1.png new file mode 100644 index 0000000..87d40f8 Binary files /dev/null and b/supplementary_fig02_files/figure-commonmark/unnamed-chunk-27-1.png differ