add enrichments

add description

README.md

@@ -36,13 +36,13 @@ _Figure 1: Example of generated figures. **(A)** Exemplary visualization of the
 
 Raw sequencing data for constant-acetate experiments at 35°C and 40°C were obtained from (Zhang et al., 2022). Raw sequencing data for constant-acetate experiment at 25°C and acetate-depleting experiments at 25°C, 35°C, and 40°C were collected in this study and are available at JGI_XXX.
 RNA libraries were prepared and sequenced by the Joint Genome Institute (JGI, Community Science Program) using the NovaSeq platform generating 150-nt paired-end reads. Samples were quality control filtered using the JGI BBDuk and BBMap pipelines (Bushnell et al.). Samples were quality assessed using FastQC (Andrews) and mapped to the Chlamydomonas reinhardtii v5.6 genome (Merchant et al. 2007) using HISAT2 version 2.2.0 (Kim et al., 2015). Reads per feature were counted via featureCounts (Liao et al., 2014). The count matrix was combined with existing data (Zhang 2022), resulting in a 16,403x101 count matrix. Prior to imputation of two missing time points in the constant-acetate 25°C experiment, transcripts were filtered to have nonzero counts in at least 90 % of the samples. 
- 
+
 ### Imputation
 Measurements for time points 4h and 8h are missing for the constant-acetate 25°C time course. Beside preheat, 2h, and 24h samples, additional samples were taken for the constant-acetate 25°C time course at time points 0h, 0.5h, 1h, 26h, and 48h. After ensuring a high correlation (corr >= 0.993), the two missing time points were imputed as follows: For each transcript, two of the additional timepoint-triplicates were sampled randomly. It was ensured that not both missing timepoints were imputed with the same count data. The final count matrix consists of 14,893 transcripts in 90 samples (5 time points measured at 6 conditions as triplicates). 
- 
+
 ### Statistical testing
-Imputed count data were tested for differential expression using DESeq2 v1.38.3 (Love et al., 2014). The following tests were performed: (i) constant-acetate 25°C vs constant-acetate 35°C; (ii) constant-acetate 25°C vs constant-acetate 40°C; (iii) acetate-depleting 25°C vs acetate-depleting 35°C; (iv) acetate-depleting 25°C vs acetate-depleting 40°C; (v) (constant-acetate 35°C and acetate-depleting 35°C) vs (constant-acetate 40°C and acetate-depleting 40°C); (vi) (constant-acetate 35°C and constant-acetate 40°C) vs (acetate-depleting 35°C and acetate-depleting 40°C); (vii) interaction of v and vi. 
- 
+Imputed count data were tested for differential expression using multifactor designs in DESeq2 v1.38.3 (Love et al., 2014). The following tests were performed: (i) constant-acetate 25°C vs constant-acetate 35°C; (ii) constant-acetate 25°C vs constant-acetate 40°C; (iii) acetate-depleting 25°C vs acetate-depleting 35°C; (iv) acetate-depleting 25°C vs acetate-depleting 40°C; (v) (constant-acetate 35°C and acetate-depleting 35°C) vs (constant-acetate 40°C and acetate-depleting 40°C); (vi) (constant-acetate 35°C and constant-acetate 40°C) vs (acetate-depleting 35°C and acetate-depleting 40°C); (vii) interaction of v and vi; and (viii) acetate-depleting 25°C vs constant-acetate 25°C. 
+
 ### Sample normalization
 The normalization of the count matrix was conducted using the median of ratios method (Love et al., 2014).
  
@@ -55,12 +55,16 @@ PCA was performed on averaged triplicates using FSharp.Statsv0.4.11 on transcrip
 ### Functional set figures
 Functional descriptions were determined for each transcript (Merchant et al., 2007; Usadel et al., 2009; Venn and Muehlhaus, 2022b). Transcripts were grouped according to their functional description and time courses of their averaged normed counts were visualized as z score and log2 fold change respectively. An ANOVA was performed for each transcript at each treatment to elucidate whether a transcript underwent a relevant change during its time course (Venn et al., 2022a).  
  
+### Ontology enrichments
+Ontology enrichment was performed using extended MapMan annotations (e.g. "PS.lightreaction.LHC" became "PS.Lightreaction.LHC", "PS.Lightreaction" and "PS"). The measured and filtered transcripts served as background. If a transcript showed significant differential expression in the respective comparison (FDR < 0.05), it was considered as significant for its annotations. Enrichment p values were determined using hypergeometric tests. Multiple testing correction was performed using the Benjamini-Hochberg method (Benjamini & Hochberg 1995; Venn et al., 2022a).
+
 ### Visualization
 Heatmaps, PCA, and functional sets figures were created using Plotly.NETv4.0.0 (Schneider et al., 2022).
  
 ### References:
 - Benedikt Venn, Lukas Weil, Kevin Schneider, David Zimmer & Timo Mühlhaus. (2022a). fslaborg/FSharp.Stats. Zenodo. https://doi.org/10.5281/zenodo.6337056 
 - Benedikt Venn & Timo Mühlhaus (2022b), CSBiology/OntologyEnrichment: Release 0.0.1 (0.0.1). Zenodo. https://doi.org/10.5281/zenodo.6340412
+- Benjamini, Yoav, and Yosef Hochberg. "Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing." Journal of the Royal Statistical Society. Series B (Methodological), vol. 57, no. 1, 1995, pp. 289–300. JSTOR, http://www.jstor.org/stable/2346101..
 - Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014). https://doi.org/10.1186/s13059-014-0550-8 
 - Andrews, S. (n.d.). FastQC A Quality Control tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 - BBDuk: https://sourceforge.net/projects/bbmap/

runs/05_Enrichments/Acetate-depleting-25vs35.html

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+    var data = [{"type":"bar","x":[1.3250842190794538,1.3520503454038568,1.3947827290531736,1.4161526379852183,1.4005019635445202,1.4005019635445202,1.4005019635445202,1.386290110644495,1.4797276795308587,1.5098845627583342,1.5417591749880655,1.5484108884987497,1.6404848927756226,1.6633448452165591,1.6613607448250098,1.6529135799688177,1.7306590968497277,1.7933401498963302,1.835198604107152,1.9963253994297985,1.9963253994297985,2.179812766418218,2.148881593814549,2.2369995269389578,2.4201453177112446,2.512864286635501,2.549298322184172,2.7645671464111263,2.860623334002075,2.9810311883037968,3.4188160010440423,4.140166835137583,4.49254210622774,4.688580037397053,4.961504632904725,4.878486898643194,5.811283902853119],"y":["lipid metabolism","protein.degradation.metalloprotease","protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs","nucleotide metabolism.deoxynucleotide metabolism","misc.myrosinases-lectin-jacalin","cell.motility.eukaryotes.radial spoke","cell.organisation.cytoskeleton.mikrotubuli","misc.nitrilases, nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases","misc.rhodanese","PS.carbon concentrating mechanism","RNA.regulation of transcription.putative transcription regulator","cell wall","transport.metal","S-assimilation.APS","protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit","RNA.regulation of transcription.MYB domain transcription factor family","lipid metabolism.FA synthesis and FA elongation","protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications","transport.ABC transporters and multidrug resistance systems","protein.synthesis.ribosomal protein.prokaryotic.non-organellar","amino acid metabolism.degradation.aromatic aa","lipid metabolism.lipid degradation","cell.motility.eukaryotes.intraflagellar transport","cell","cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex B","protein.synthesis.ribosome biogenesis","cell.organisation","signalling.receptor kinases","cell.motility.eukaryotes.intraflagellar transport.IFT particle protein","protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit","cell.motility.eukaryotes.basal bodies","lipid metabolism.lipid degradation.beta-oxidation","DNA.synthesis/chromatin structure","protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit","protein.synthesis.ribosomal protein.prokaryotic","DNA","protein.synthesis.ribosomal protein.prokaryotic.chloroplast"],"text":["99/228","42/89","7/10","11/18","10/16","10/16","10/16","8/12","14/24","25/48","26/50","22/41","25/47","13/21","9/13","12/19","32/62","30/57","49/100","9/12","9/12","34/63","15/23","325/769","9/11","<b>54/105 *</b>","<b>94/197 *</b>","<b>50/94 *</b>","<b>13/17 *</b>","<b>9/10 *</b>","<b>22/32 **</b>","<b>12/13 **</b>","<b>111/216 **</b>","<b>20/25 **</b>","<b>43/67 **</b>","<b>176/361 **</b>","<b>29/38 **</b>"],"textposition":"inside","orientation":"h","marker":{"color":"rgba(2, 138, 115, 1.0)","pattern":{}}}];
+    var layout = {"width":1000,"height":1000,"template":{"layout":{"paper_bgcolor":"white","plot_bgcolor":"white","xaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true},"yaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true}},"data":{}},"margin":{"l":500.0},"xaxis":{"title":{"text":"-log<sub>10</sub> (p value)"}}};
+    var config = {"responsive":true,"toImageButtonOptions":{"format":"svg"}};
+    Plotly.newPlot('f1927498-07c1-462d-bc51-215cc4070454', data, layout, config);
+};
+renderPlotly_f192749807c1462dbc51215cc4070454();
+</script><p style="font-family: Arial, sans-serif;width:900px;"><b>MapMan ontology enrichment</b> <br><br>Ontology enrichment was performed using the extended MapMan ontology.
+                The p values were calculated using a hypergeometric test (<a href="https://github.com/CSBiology/BioFSharp">BioFSharp.Stats</a>) and corrected for multiple testing using the Benjamini-Hochberg method (<a href="https://github.com/fslaborg/FSharp.Stats">FSharp.Stats</a>). <br> 
+                <br> All functional sets with a p value less than 0.05 and more than 10 annotated transcripts are shown. 
+                The ratio within the bars indicate the number of significant transcripts vs transcripts contained in the respective bin. <br><br>FDR significant bin numbers are written bold:<br> * FDR < 0.1 <br> ** FDR < 0.05</p></body></html>
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runs/05_Enrichments/Acetate-depleting-25vs40.html

+<!DOCTYPE html>
+<html><head><script src="https://cdn.plot.ly/plotly-2.18.1.min.js"></script><title>Plotly.NET Datavisualization</title><meta charset="UTF-8"><meta name="description" content="A plotly.js graph generated with Plotly.NET"><link id="favicon" rel="shortcut icon" type="image/png" href="data:image/png;base64,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"></head><body><div id="a099a0dc-b1ed-411d-a82d-8195476498a6"><!-- Plotly chart will be drawn inside this DIV --></div><script type="text/javascript">var renderPlotly_a099a0dcb1ed411da82d8195476498a6 = function() {
+    var data = [{"type":"bar","x":[1.3516234730675416,1.4488552935034062,1.4518275988347604,1.4654657347816706,1.480269957923171,1.53984717166898,1.6131648047778857,1.6680124474346363,1.7347983115067582,1.7510083124004536,1.8003006817877893,1.9168351933070913,1.9718847184200967,1.9650640203375023,2.0297884269094846,2.114475573817676,2.094410204350278,2.1838027907016864,2.2389234750016147,2.393592430612365,2.4794363265320962,2.4794363265320962,2.6208209898402366,2.6688566284975743,2.6239383378766137,2.907521001333216,2.9386881467500525,3.066691092436732,3.31990908005195,3.4767975896563006,3.456054620917225,3.903319774486347,4.048319410446707,4.204956403169572,5.583536063932411,5.919985004033434],"y":["RNA.processing.RNA helicase","RNA.regulation of transcription.putative transcription regulator","cell.division","amino acid metabolism.synthesis.branched chain group","hormone metabolism.abscisic acid","amino acid metabolism.synthesis.aspartate family.lysine","cell.motility.eukaryotes.basal bodies","RNA.RNA binding","TCA / organic transformation.TCA","cell.motility.eukaryotes.intraflagellar transport.IFT particle protein.complex B","amino acid metabolism.synthesis.aspartate family","RNA","protein.degradation.serine protease","protein.synthesis.ribosomal protein.prokaryotic.non-organellar","RNA.processing","DNA.synthesis/chromatin structure","mitochondrial electron transport / ATP synthesis","transport.p- and v-ATPases","transport.p- and v-ATPases.H+-transporting two-sector ATPase","cell.organisation","protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs","protein.synthesis.ribosomal protein.prokaryotic.non-organellar.50S subunit","transport.unspecified anions","DNA","protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications","mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear","protein.synthesis.ribosome biogenesis","cell.motility.eukaryotes.intraflagellar transport.IFT particle protein","protein.synthesis.initiation","cell.motility.eukaryotes.intraflagellar transport","mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I","protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit","protein.synthesis.ribosomal protein.prokaryotic","protein.synthesis.ribosomal protein.prokaryotic.chloroplast","protein.synthesis","mitochondrial electron transport / ATP synthesis.NADH-DH (type I)"],"text":["29/41","35/50","61/92","11/13","23/31","9/10","24/32","62/92","21/27","10/11","31/42","596/993","45/63","11/12","169/265","140/216","88/131","32/42","15/17","130/197","<b>10/10 *</b>","<b>10/10 *</b>","<b>14/15 *</b>","<b>231/361 *</b>","<b>43/57 *</b>","<b>21/24 *</b>","<b>75/105 *</b>","<b>16/17 **</b>","<b>46/59 **</b>","<b>21/23 **</b>","<b>29/34 **</b>","<b>23/25 **</b>","<b>53/67 **</b>","<b>33/38 **</b>","<b>267/394 **</b>","<b>50/58 **</b>"],"textposition":"inside","orientation":"h","marker":{"color":"rgba(2, 138, 115, 1.0)","pattern":{}}}];
+    var layout = {"width":1000,"height":1000,"template":{"layout":{"paper_bgcolor":"white","plot_bgcolor":"white","xaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true},"yaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true}},"data":{}},"margin":{"l":500.0},"xaxis":{"title":{"text":"-log<sub>10</sub> (p value)"}}};
+    var config = {"responsive":true,"toImageButtonOptions":{"format":"svg"}};
+    Plotly.newPlot('a099a0dc-b1ed-411d-a82d-8195476498a6', data, layout, config);
+};
+renderPlotly_a099a0dcb1ed411da82d8195476498a6();
+</script><p style="font-family: Arial, sans-serif;width:900px;"><b>MapMan ontology enrichment</b> <br><br>Ontology enrichment was performed using the extended MapMan ontology.
+                The p values were calculated using a hypergeometric test (<a href="https://github.com/CSBiology/BioFSharp">BioFSharp.Stats</a>) and corrected for multiple testing using the Benjamini-Hochberg method (<a href="https://github.com/fslaborg/FSharp.Stats">FSharp.Stats</a>). <br> 
+                <br> All functional sets with a p value less than 0.05 and more than 10 annotated transcripts are shown. 
+                The ratio within the bars indicate the number of significant transcripts vs transcripts contained in the respective bin. <br><br>FDR significant bin numbers are written bold:<br> * FDR < 0.1 <br> ** FDR < 0.05</p></body></html>
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runs/05_Enrichments/Acetate-depleting-25vsConstant-acetate-25.html

+<!DOCTYPE html>
+<html><head><script src="https://cdn.plot.ly/plotly-2.18.1.min.js"></script><title>Plotly.NET Datavisualization</title><meta charset="UTF-8"><meta name="description" content="A plotly.js graph generated with Plotly.NET"><link id="favicon" rel="shortcut icon" type="image/png" href="data:image/png;base64,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"></head><body><div id="660a7db9-c290-4dbd-ab3e-3f80a2947649"><!-- Plotly chart will be drawn inside this DIV --></div><script type="text/javascript">var renderPlotly_660a7db9c2904dbdab3e3f80a2947649 = function() {
+    var data = [{"type":"bar","x":[1.3512485592467198,1.3316909898216345,1.307891564430785,1.3846557759872105,1.423462731745255,1.423462731745255,1.5054873684833325,1.5387978111916019,1.5336234022278188,1.5899526339762171,1.6259170497271642,1.6402592118791706,1.6155781039981942,1.7925445998307699,1.8655154167217616,1.809148765280439,1.7771816971369354,1.9450312765771387,2.002362918153693,2.308510853714928,2.303892311904962,2.446648441479741,2.5853245914670744,2.566222621208845,3.2319888660872165,3.405447735096568,3.405447735096568,3.835153810917606,5.359405602204382],"y":["cell","protein.synthesis.initiation","protein.synthesis.ribosomal protein","redox.thioredoxin","mitochondrial electron transport / ATP synthesis.cytochrome c oxidase","amino acid metabolism.degradation.branched chain group","RNA.RNA binding","RNA","protein.synthesis.ribosomal protein.prokaryotic.unknown organellar","redox","protein.synthesis","transport.metal","protein.folding.prefoldin and trigger factor","PS.lightreaction.photosystem I","not assigned.no ontology","cell.motility.eukaryotes.axonemal dyneins.outer arm","TCA / organic transformation.TCA.pyruvate DH","not assigned","PS.lightreaction","cell.motility.eukaryotes.other","protein.synthesis.ribosomal protein.prokaryotic","PS","misc.myrosinases-lectin-jacalin","mitochondrial electron transport / ATP synthesis","cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species","cell.motility.eukaryotes","cell.motility","cell.motility.eukaryotes.axonemal dyneins.inner arm","cell.motility.eukaryotes.axonemal dyneins"],"text":["552/769","47/59","139/186","39/48","17/19","17/19","72/92","712/993","14/15","106/138","290/394","39/47","10/10","20/22","57/70","16/17","11/11","58/71","127/164","32/36","56/67","200/261","16/16","105/131","<b>20/20 *</b>","<b>226/290 **</b>","<b>226/290 **</b>","<b>30/31 **</b>","<b>46/48 **</b>"],"textposition":"inside","orientation":"h","marker":{"color":"rgba(2, 138, 115, 1.0)","pattern":{}}}];
+    var layout = {"width":1000,"height":1000,"template":{"layout":{"paper_bgcolor":"white","plot_bgcolor":"white","xaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true},"yaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true}},"data":{}},"margin":{"l":500.0},"xaxis":{"title":{"text":"-log<sub>10</sub> (p value)"}}};
+    var config = {"responsive":true,"toImageButtonOptions":{"format":"svg"}};
+    Plotly.newPlot('660a7db9-c290-4dbd-ab3e-3f80a2947649', data, layout, config);
+};
+renderPlotly_660a7db9c2904dbdab3e3f80a2947649();
+</script><p style="font-family: Arial, sans-serif;width:900px;"><b>MapMan ontology enrichment</b> <br><br>Ontology enrichment was performed using the extended MapMan ontology.
+                The p values were calculated using a hypergeometric test (<a href="https://github.com/CSBiology/BioFSharp">BioFSharp.Stats</a>) and corrected for multiple testing using the Benjamini-Hochberg method (<a href="https://github.com/fslaborg/FSharp.Stats">FSharp.Stats</a>). <br> 
+                <br> All functional sets with a p value less than 0.05 and more than 10 annotated transcripts are shown. 
+                The ratio within the bars indicate the number of significant transcripts vs transcripts contained in the respective bin. <br><br>FDR significant bin numbers are written bold:<br> * FDR < 0.1 <br> ** FDR < 0.05</p></body></html>
\ No newline at end of file

runs/05_Enrichments/Constant-acetate-25vs35.html

+<!DOCTYPE html>
+<html><head><script src="https://cdn.plot.ly/plotly-2.18.1.min.js"></script><title>Plotly.NET Datavisualization</title><meta charset="UTF-8"><meta name="description" content="A plotly.js graph generated with Plotly.NET"><link id="favicon" rel="shortcut icon" type="image/png" href="data:image/png;base64,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"></head><body><div id="57a17807-be0a-429a-aca7-90b24a1c64d2"><!-- Plotly chart will be drawn inside this DIV --></div><script type="text/javascript">var renderPlotly_57a17807be0a429aaca790b24a1c64d2 = function() {
+    var data = [{"type":"bar","x":[1.327877080988439,1.342969994688088,1.3916935197363267,1.460883980128096,1.3922154505953472,1.4112236983275261,1.6202351785366333,1.589086411017176,1.6202351785366333,1.5675115785298575,1.6726648665043458,1.7006440941561485,1.6915178729817135,1.8472431675823986,1.9079092040902919,1.9566502772665904,1.9574095001720009,2.002323264068157,2.1745316552890435,2.153208302491251,2.3927238581733357,2.3690586968903635,2.5792403064471667,2.8433270649773235,3.7944228044432613,4.14039249647291,4.184051611313486,6.51592310741251],"y":["RNA.regulation of transcription.MYB domain transcription factor family","RNA.regulation of transcription.putative transcription regulator","protein.degradation.metalloprotease","cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species","signalling.MAP kinases","RNA.processing","protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit","protein.synthesis.ribosomal protein.unknown","lipid metabolism.lipid degradation.beta-oxidation","RNA.regulation of transcription.unclassified","cell","RNA.processing.ribonucleases","transport.metal","cell.division","cell.motility.eukaryotes.axonemal dyneins.inner arm","protein.synthesis.ribosomal protein.prokaryotic.unknown organellar","protein.folding.prefoldin and trigger factor","protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications","cell.motility.eukaryotes.axonemal dyneins","protein.synthesis.ribosomal protein.prokaryotic.unknown organellar.50S subunit","protein.synthesis.ribosomal protein","protein.synthesis.ribosome biogenesis","RNA.regulation of transcription","protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit","protein.synthesis","RNA","protein.synthesis.ribosomal protein.prokaryotic.chloroplast","protein.synthesis.ribosomal protein.prokaryotic"],"text":["16/19","38/50","65/89","17/20","84/117","183/265","12/13","15/17","12/13","74/101","517/769","27/33","37/47","69/92","26/31","14/15","10/10","45/57","39/48","11/11","136/186","80/105","405/585","23/25","<b>285/394 **</b>","<b>689/993 **</b>","<b>35/38 **</b>","<b>61/67 **</b>"],"textposition":"inside","orientation":"h","marker":{"color":"rgba(2, 138, 115, 1.0)","pattern":{}}}];
+    var layout = {"width":1000,"height":1000,"template":{"layout":{"paper_bgcolor":"white","plot_bgcolor":"white","xaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true},"yaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true}},"data":{}},"margin":{"l":500.0},"xaxis":{"title":{"text":"-log<sub>10</sub> (p value)"}}};
+    var config = {"responsive":true,"toImageButtonOptions":{"format":"svg"}};
+    Plotly.newPlot('57a17807-be0a-429a-aca7-90b24a1c64d2', data, layout, config);
+};
+renderPlotly_57a17807be0a429aaca790b24a1c64d2();
+</script><p style="font-family: Arial, sans-serif;width:900px;"><b>MapMan ontology enrichment</b> <br><br>Ontology enrichment was performed using the extended MapMan ontology.
+                The p values were calculated using a hypergeometric test (<a href="https://github.com/CSBiology/BioFSharp">BioFSharp.Stats</a>) and corrected for multiple testing using the Benjamini-Hochberg method (<a href="https://github.com/fslaborg/FSharp.Stats">FSharp.Stats</a>). <br> 
+                <br> All functional sets with a p value less than 0.05 and more than 10 annotated transcripts are shown. 
+                The ratio within the bars indicate the number of significant transcripts vs transcripts contained in the respective bin. <br><br>FDR significant bin numbers are written bold:<br> * FDR < 0.1 <br> ** FDR < 0.05</p></body></html>
\ No newline at end of file

runs/05_Enrichments/Constant-acetate-25vs40.html

+<!DOCTYPE html>
+<html><head><script src="https://cdn.plot.ly/plotly-2.18.1.min.js"></script><title>Plotly.NET Datavisualization</title><meta charset="UTF-8"><meta name="description" content="A plotly.js graph generated with Plotly.NET"><link id="favicon" rel="shortcut icon" type="image/png" href="data:image/png;base64,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"></head><body><div id="7bf92a6d-aea7-4b9c-ae8d-811a20daa3ae"><!-- Plotly chart will be drawn inside this DIV --></div><script type="text/javascript">var renderPlotly_7bf92a6daea74b9cae8d811a20daa3ae = function() {
+    var data = [{"type":"bar","x":[1.3364329485282864,1.302188203640598,1.302188203640598,1.302188203640598,1.302188203640598,1.4907968970587253,1.4771377137136252,1.5175819255973042,1.5616621252182423,1.5627033505943926,1.5491472403099473,1.5805169790935008,1.7056033618483797,1.7056033618483797,1.702004205705329,1.6929706174934729,1.8636335680456646,1.7007440843758967,1.8067601853630584,2.080926089578609,2.153193431163242,2.286242032116802,2.8244460576661075,4.197901329936686,4.53678636772767],"y":["PS.carbon concentrating mechanism","misc.acyl transferases","protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs","misc.O-methyl transferases","protein.folding.prefoldin and trigger factor","mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear","RNA.processing.splicing","not assigned.no ontology","RNA.processing.RNA helicase","secondary metabolism.N misc","RNA.transcription","not assigned","cell.motility.eukaryotes.axonemal dyneins","misc.oxidases - copper, flavone etc","cell.motility.eukaryotes.axonemal dyneins.inner arm.monomeric species","protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit","RNA.regulation of transcription.putative transcription regulator","cell.vesicle transport","protein.degradation.metalloprotease","mitochondrial electron transport / ATP synthesis.NADH-DH (type I)","protein.degradation.ubiquitin.E2","protein.synthesis.ribosomal protein.prokaryotic.chloroplast","protein.synthesis.ribosomal protein.prokaryotic","RNA","RNA.processing"],"text":["41/48","10/10","10/10","10/10","10/10","22/24","43/50","59/70","36/41","12/12","44/51","60/71","42/48","42/48","19/20","13/13","44/50","58/68","75/89","51/58","23/24","35/38","60/67","<b>787/993 **</b>","<b>224/265 **</b>"],"textposition":"inside","orientation":"h","marker":{"color":"rgba(2, 138, 115, 1.0)","pattern":{}}}];
+    var layout = {"width":1000,"height":1000,"template":{"layout":{"paper_bgcolor":"white","plot_bgcolor":"white","xaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true},"yaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true}},"data":{}},"margin":{"l":500.0},"xaxis":{"title":{"text":"-log<sub>10</sub> (p value)"}}};
+    var config = {"responsive":true,"toImageButtonOptions":{"format":"svg"}};
+    Plotly.newPlot('7bf92a6d-aea7-4b9c-ae8d-811a20daa3ae', data, layout, config);
+};
+renderPlotly_7bf92a6daea74b9cae8d811a20daa3ae();
+</script><p style="font-family: Arial, sans-serif;width:900px;"><b>MapMan ontology enrichment</b> <br><br>Ontology enrichment was performed using the extended MapMan ontology.
+                The p values were calculated using a hypergeometric test (<a href="https://github.com/CSBiology/BioFSharp">BioFSharp.Stats</a>) and corrected for multiple testing using the Benjamini-Hochberg method (<a href="https://github.com/fslaborg/FSharp.Stats">FSharp.Stats</a>). <br> 
+                <br> All functional sets with a p value less than 0.05 and more than 10 annotated transcripts are shown. 
+                The ratio within the bars indicate the number of significant transcripts vs transcripts contained in the respective bin. <br><br>FDR significant bin numbers are written bold:<br> * FDR < 0.1 <br> ** FDR < 0.05</p></body></html>
\ No newline at end of file

runs/05_Enrichments/Interaction.html

+<!DOCTYPE html>
+<html><head><script src="https://cdn.plot.ly/plotly-2.18.1.min.js"></script><title>Plotly.NET Datavisualization</title><meta charset="UTF-8"><meta name="description" content="A plotly.js graph generated with Plotly.NET"><link id="favicon" rel="shortcut icon" type="image/png" href="data:image/png;base64,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"></head><body><div id="50f26e67-031d-4179-8f7e-438c63fab32b"><!-- Plotly chart will be drawn inside this DIV --></div><script type="text/javascript">var renderPlotly_50f26e67031d41798f7e438c63fab32b = function() {
+    var data = [{"type":"bar","x":[1.3842906522529275,1.5097438376166716,1.6603601788755624,1.8498196310485073,1.7807630612509027,2.0788602006855808,2.507463953437125,2.9423749151924232],"y":["protein.degradation.metalloprotease","protein.degradation","lipid metabolism.lipid degradation","TCA / organic transformation","transport","lipid metabolism.lipid degradation.lipases","transport.phosphate","lipid metabolism.lipid degradation.lipases.triacylglycerol lipase"],"text":["<b>2/89 *</b>","<b>6/653 *</b>","<b>2/63 **</b>","<b>2/50 **</b>","<b>6/565 **</b>","<b>2/38 **</b>","<b>2/23 **</b>","<b>2/14 **</b>"],"textposition":"inside","orientation":"h","marker":{"color":"rgba(2, 138, 115, 1.0)","pattern":{}}}];
+    var layout = {"width":1000,"height":1000,"template":{"layout":{"paper_bgcolor":"white","plot_bgcolor":"white","xaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true},"yaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true}},"data":{}},"margin":{"l":500.0},"xaxis":{"title":{"text":"-log<sub>10</sub> (p value)"}}};
+    var config = {"responsive":true,"toImageButtonOptions":{"format":"svg"}};
+    Plotly.newPlot('50f26e67-031d-4179-8f7e-438c63fab32b', data, layout, config);
+};
+renderPlotly_50f26e67031d41798f7e438c63fab32b();
+</script><p style="font-family: Arial, sans-serif;width:900px;"><b>MapMan ontology enrichment</b> <br><br>Ontology enrichment was performed using the extended MapMan ontology.
+                The p values were calculated using a hypergeometric test (<a href="https://github.com/CSBiology/BioFSharp">BioFSharp.Stats</a>) and corrected for multiple testing using the Benjamini-Hochberg method (<a href="https://github.com/fslaborg/FSharp.Stats">FSharp.Stats</a>). <br> 
+                <br> All functional sets with a p value less than 0.05 and more than 10 annotated transcripts are shown. 
+                The ratio within the bars indicate the number of significant transcripts vs transcripts contained in the respective bin. <br><br>FDR significant bin numbers are written bold:<br> * FDR < 0.1 <br> ** FDR < 0.05</p></body></html>
\ No newline at end of file

runs/05_Enrichments/Medium.html

+<!DOCTYPE html>
+<html><head><script src="https://cdn.plot.ly/plotly-2.18.1.min.js"></script><title>Plotly.NET Datavisualization</title><meta charset="UTF-8"><meta name="description" content="A plotly.js graph generated with Plotly.NET"><link id="favicon" rel="shortcut icon" type="image/png" href="data:image/png;base64,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"></head><body><div id="13d19dbc-da98-47f8-84c9-967fda48d1e4"><!-- Plotly chart will be drawn inside this DIV --></div><script type="text/javascript">var renderPlotly_13d19dbcda9847f884c9967fda48d1e4 = function() {
+    var data = [{"type":"bar","x":[1.321094680581338,1.4914750117042017,1.5292215738666406,1.6410910167131947,1.5515184237781416,1.6215538389104691,1.5292215738666406,1.8926701460155786,1.866764117664291,1.8082904105462123,2.3847603346221855,2.5090312970738835],"y":["lipid metabolism.lipid degradation","PS.carbon concentrating mechanism.algal","S-assimilation.APS","protein.degradation","protein.degradation.metalloprotease","PS.carbon concentrating mechanism","PS.lightreaction.unspecified.TEF","lipid metabolism.lipid degradation.lipases","lipid metabolism.lipid degradation.lipases.triacylglycerol lipase","transport.unspecified anions","signalling.MAP kinases","transport.phosphate"],"text":["3/63","2/22","2/21","15/653","4/89","3/48","2/21","3/38","2/14","2/15","<b>6/117 *</b>","<b>3/23 *</b>"],"textposition":"inside","orientation":"h","marker":{"color":"rgba(2, 138, 115, 1.0)","pattern":{}}}];
+    var layout = {"width":1000,"height":1000,"template":{"layout":{"paper_bgcolor":"white","plot_bgcolor":"white","xaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true},"yaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true}},"data":{}},"margin":{"l":500.0},"xaxis":{"title":{"text":"-log<sub>10</sub> (p value)"}}};
+    var config = {"responsive":true,"toImageButtonOptions":{"format":"svg"}};
+    Plotly.newPlot('13d19dbc-da98-47f8-84c9-967fda48d1e4', data, layout, config);
+};
+renderPlotly_13d19dbcda9847f884c9967fda48d1e4();
+</script><p style="font-family: Arial, sans-serif;width:900px;"><b>MapMan ontology enrichment</b> <br><br>Ontology enrichment was performed using the extended MapMan ontology.
+                The p values were calculated using a hypergeometric test (<a href="https://github.com/CSBiology/BioFSharp">BioFSharp.Stats</a>) and corrected for multiple testing using the Benjamini-Hochberg method (<a href="https://github.com/fslaborg/FSharp.Stats">FSharp.Stats</a>). <br> 
+                <br> All functional sets with a p value less than 0.05 and more than 10 annotated transcripts are shown. 
+                The ratio within the bars indicate the number of significant transcripts vs transcripts contained in the respective bin. <br><br>FDR significant bin numbers are written bold:<br> * FDR < 0.1 <br> ** FDR < 0.05</p></body></html>
\ No newline at end of file

runs/05_Enrichments/Temperature.html

+<!DOCTYPE html>
+<html><head><script src="https://cdn.plot.ly/plotly-2.18.1.min.js"></script><title>Plotly.NET Datavisualization</title><meta charset="UTF-8"><meta name="description" content="A plotly.js graph generated with Plotly.NET"><link id="favicon" rel="shortcut icon" type="image/png" href="data:image/png;base64,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"></head><body><div id="bc555446-1090-458c-bded-9fbc8d19b948"><!-- Plotly chart will be drawn inside this DIV --></div><script type="text/javascript">var renderPlotly_bc5554461090458cbded9fbc8d19b948 = function() {
+    var data = [{"type":"bar","x":[1.309351019006195,1.3839980752892795,1.4074474164825819,1.459980184969131,1.4549716561927657,1.4936127081736204,1.5491442167273113,1.6053146598742676,1.6187117849672075,1.6495799356740917,1.654126053493457,1.6682596682394586,1.6924037577118836,1.7177762443470188,1.8382669041069595,1.8745099492906059,1.9359094617912902,1.9506994323559828,2.0967063277416766,2.115724611102774,2.2482457724877554,2.1865857357973866,2.2482457724877554,2.221043421370095,2.1865857357973866,2.218268350246134,2.1830406997080716,2.425003022004279,2.524914510311768,2.5916764391974163,2.7014003877414514,2.8716658121911465,3.0156464908117493,3.103650240689721,3.9715380540716914,4.114670281629256,4.128656833490756,4.364748505731961,4.5933294009969226,7.708625668354397,10.0,10.0],"y":["secondary metabolism.isoprenoids.carotenoids","amino acid metabolism.synthesis","nucleotide metabolism.degradation","glycolysis.unclear/dually targeted","transport.metabolite transporters at the envelope membrane","transport.metal","glycolysis","protein.targeting.mitochondria","protein.targeting","lipid metabolism.phospholipid synthesis","lipid metabolism.lipid degradation.lipases","RNA.regulation of transcription.HDA","protein.folding.immunophilins (IMM).FKBPs","protein.synthesis.ribosome biogenesis.pre-rRNA processing and modifications.snoRNPs","transport.p- and v-ATPases","TCA / organic transformation.other organic acid transformations","transport.metabolite transporters at the mitochondrial membrane","PS.lightreaction.photosystem I.LHC-I","amino acid metabolism","lipid metabolism","mitochondrial electron transport / ATP synthesis.cytochrome c oxidase","gluconeogenesis / glyoxylate cycle","amino acid metabolism.degradation.branched chain group","protein.synthesis.ribosomal protein.prokaryotic.chloroplast.50S subunit","misc.nitrilases, nitrile lyases, berberine bridge enzymes, reticuline oxidases, troponine reductases","amino acid metabolism.synthesis.aspartate family","lipid metabolism.lipid degradation","protein.synthesis.ribosomal protein.prokaryotic.chloroplast.30S subunit","mitochondrial electron transport / ATP synthesis.F1-ATPase","TCA / organic transformation.TCA","amino acid metabolism.synthesis.aspartate family.lysine","PS.lightreaction.photosystem I","TCA / organic transformation","protein.synthesis.initiation","transport","protein.synthesis.ribosomal protein.prokaryotic.chloroplast","mitochondrial electron transport / ATP synthesis.NADH-DH (type I).localisation not clear","protein.synthesis.ribosomal protein.prokaryotic","transport.p- and v-ATPases.H+-transporting two-sector ATPase","mitochondrial electron transport / ATP synthesis.NADH-DH (type I).complex I","mitochondrial electron transport / ATP synthesis","mitochondrial electron transport / ATP synthesis.NADH-DH (type I)"],"text":["18/25","91/149","17/23","10/12","19/26","32/47","43/65","20/27","120/197","22/30","27/38","15/19","17/22","9/10","30/42","12/14","34/48","10/11","138/223","141/228","16/19","11/12","16/19","20/25","11/12","31/42","44/63","<b>12/13 *</b>","<b>15/17 *</b>","<b>22/27 *</b>","<b>10/10 *</b>","<b>19/22 *</b>","<b>38/50 **</b>","<b>44/59 **</b>","<b>347/565 **</b>","<b>32/38 **</b>","<b>22/24 **</b>","<b>52/67 **</b>","<b>17/17 **</b>","<b>33/34 **</b>","<b>108/131 **</b>","<b>55/58 **</b>"],"textposition":"inside","orientation":"h","marker":{"color":"rgba(2, 138, 115, 1.0)","pattern":{}}}];
+    var layout = {"width":1000,"height":1000,"template":{"layout":{"paper_bgcolor":"white","plot_bgcolor":"white","xaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true},"yaxis":{"ticks":"inside","mirror":"all","showline":true,"zeroline":true}},"data":{}},"margin":{"l":500.0},"xaxis":{"title":{"text":"-log<sub>10</sub> (p value)"}}};
+    var config = {"responsive":true,"toImageButtonOptions":{"format":"svg"}};
+    Plotly.newPlot('bc555446-1090-458c-bded-9fbc8d19b948', data, layout, config);
+};
+renderPlotly_bc5554461090458cbded9fbc8d19b948();
+</script><p style="font-family: Arial, sans-serif;width:900px;"><b>MapMan ontology enrichment</b> <br><br>Ontology enrichment was performed using the extended MapMan ontology.
+                The p values were calculated using a hypergeometric test (<a href="https://github.com/CSBiology/BioFSharp">BioFSharp.Stats</a>) and corrected for multiple testing using the Benjamini-Hochberg method (<a href="https://github.com/fslaborg/FSharp.Stats">FSharp.Stats</a>). <br> 
+                <br> All functional sets with a p value less than 0.05 and more than 10 annotated transcripts are shown. 
+                The ratio within the bars indicate the number of significant transcripts vs transcripts contained in the respective bin. <br><br>FDR significant bin numbers are written bold:<br> * FDR < 0.1 <br> ** FDR < 0.05</p></body></html>
\ No newline at end of file