diff --git a/docs/articles/Omix_vignette_MAP_CV_pseudotemporal.html b/docs/articles/Omix_vignette_MAP_CV_pseudotemporal.html
index 1def2fc..87996a5 100644
--- a/docs/articles/Omix_vignette_MAP_CV_pseudotemporal.html
+++ b/docs/articles/Omix_vignette_MAP_CV_pseudotemporal.html
@@ -88,7 +88,7 @@ <h1 data-toc-skip>Omix - Pseudotemporal multi-omics
                         <h4 data-toc-skip class="author">This vignette
 was created by Eléonore Schneegans and Nurun Fancy</h4>
             
-            <h4 data-toc-skip class="date">20 July, 2023</h4>
+            <h4 data-toc-skip class="date">12 January, 2024</h4>
       
       
       <div class="hidden name"><code>Omix_vignette_MAP_CV_pseudotemporal.Rmd</code></div>
@@ -171,13 +171,13 @@ <h3 id="running-omix">Running <em>Omix</em><a class="anchor" aria-label="anchor"
 <span><span class="va">GO_fp</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="va">outputDir</span>, <span class="st">"GO_Biological_Process_2021.txt"</span><span class="op">)</span></span>
 <span></span>
 <span></span>
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 <span></span>
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@@ -677,7 +677,7 @@ <h3 id="extract-features-that-are-driving-factor-6-based-on-feature-weights">Ext
 <div class="sourceCode" id="cb67"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">weights</span><span class="op">=</span><span class="fu"><a href="../reference/extract_weigths.html">extract_weigths</a></span><span class="op">(</span><span class="va">integrated_object</span>,</span>
 <span>                           factor<span class="op">=</span><span class="fl">6</span>,</span>
-<span>                           threshold<span class="op">=</span><span class="fl">0.2</span>,</span>
+<span>                           threshold<span class="op">=</span><span class="fl">1.5</span>,</span>
 <span>                           sense_check_variable<span class="op">=</span><span class="st">'PHF1'</span><span class="op">)</span></span></code></pre></div>
 <div class="section level4">
 <h4 id="weights-distribution-in-factor-6">Weights distribution in Factor 6<a class="anchor" aria-label="anchor" href="#weights-distribution-in-factor-6"></a>
@@ -721,20 +721,17 @@ <h4 id="selected-features-based-on-defined-threshold">Selected features based on
 <ul>
 <li><p><code>r</code>length(weights<span class="math inline">\(weights\)</span>ranked_weights_negative$rna)` RNAs
 have weights below -0.3 in factor 6</p></li>
-<li><p>327 proteins have weights below -0.3 in factor 6</p></li>
+<li><p>176 proteins have weights below -0.3 in factor 6</p></li>
 </ul>
 <p>Some driving features may overlap between transcriptomics and
 proteomics</p>
 <div class="sourceCode" id="cb73"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://generics.r-lib.org/reference/setops.html" class="external-link">intersect</a></span><span class="op">(</span><span class="va">weights</span><span class="op">$</span><span class="va">weights</span><span class="op">$</span><span class="va">ranked_weights_negative</span><span class="op">$</span><span class="va">rna</span>,<span class="va">weights</span><span class="op">$</span><span class="va">weights</span><span class="op">$</span><span class="va">ranked_weights_negative</span><span class="op">$</span><span class="va">protein</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">##  [1] "ANXA1"   "B2M"     "ICAM5"   "COL18A1" "S100A10" "C4A"     "GFAP"   </span></span>
-<span><span class="co">##  [8] "RLBP1"   "ITPR1"   "S100A4"  "GJA1"    "VIM"     "PRELP"   "CLIC1"  </span></span>
-<span><span class="co">## [15] "AKAP5"   "FLNA"    "HSPG2"   "CAPS"    "AHNAK"   "COL6A2"  "CAPG"   </span></span>
-<span><span class="co">## [22] "TAGLN"   "FABP7"   "C1QA"    "MYL9"    "F13A1"   "C3"      "COL14A1"</span></span>
-<span><span class="co">## [29] "OGN"     "ANXA2"   "C1QC"    "CRABP1"  "DCN"     "COL1A1"  "COL6A3" </span></span>
-<span><span class="co">## [36] "CALB2"</span></span></code></pre>
+<pre><code><span><span class="co">##  [1] "AKAP5"   "FLNA"    "HSPG2"   "AHNAK"   "COL6A2"  "CAPG"    "TAGLN"  </span></span>
+<span><span class="co">##  [8] "FABP7"   "F13A1"   "C3"      "COL14A1" "ANXA2"   "C1QC"    "CRABP1" </span></span>
+<span><span class="co">## [15] "DCN"     "COL1A1"  "CALB2"</span></span></code></pre>
 <ul>
-<li>13 features overlap between omic layers</li>
+<li>7 features overlap between omic layers</li>
 </ul>
 </div>
 </div>
@@ -785,7 +782,7 @@ <h4 id="community-detection-within-multi-omic-network">Community detection withi
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class=\"display\">\n  <thead>\n    <tr>\n      <th>community<\/th>\n      <th>feature<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"Blfrtip","buttons":["colvis",{"extend":"copy","exportOptions":{"columns":":visible"}},{"extend":"csv","exportOptions":{"columns":":visible"}},{"extend":"excel","exportOptions":{"columns":":visible"}}],"columnDefs":[],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><ul>
 <li>5 communities are detected in the multi-omics network.</li>
 <li>Most communities are omic dependent, since generally there is more
 intra omic correlation than inter omic correlation</li>
@@ -805,7 +802,7 @@ <h4 id="community-1">Community 1<a class="anchor" aria-label="anchor" href="#com
 <span>                            community<span class="op">=</span><span class="fl">1</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/interactive_network.html">interactive_network</a></span><span class="op">(</span>igraph<span class="op">=</span><span class="va">community_1</span><span class="op">$</span><span class="va">graph</span>,communities<span class="op">=</span><span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
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 <h4 id="community-4">Community 4<a class="anchor" aria-label="anchor" href="#community-4"></a>
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 </div>
 <div class="section level4">
 <h4 id="community-hubs">Community hubs<a class="anchor" aria-label="anchor" href="#community-hubs"></a>
@@ -827,56 +824,32 @@ <h4 id="community-hubs">Community hubs<a class="anchor" aria-label="anchor" href
 </ul>
 <div class="sourceCode" id="cb80"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/sort.html" class="external-link">sort</a></span><span class="op">(</span><span class="va">community_4</span><span class="op">$</span><span class="va">hubs</span>, decreasing <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">##    SLC1A5_rna    TBXAS1_rna  ARHGAP30_rna     SASH3_rna     LAIR1_rna </span></span>
-<span><span class="co">##    1.00000000    0.99373217    0.98642752    0.98435469    0.98235011 </span></span>
-<span><span class="co">##   NCKAP1L_rna     ITGB2_rna       SLA_rna     RBM47_rna       SYK_rna </span></span>
-<span><span class="co">##    0.98067378    0.97961400    0.97686353    0.97651079    0.96915836 </span></span>
-<span><span class="co">##     ALOX5_rna     HCLS1_rna    TYROBP_rna     IKZF1_rna     CD163_rna </span></span>
-<span><span class="co">##    0.96356390    0.96296850    0.95458866    0.95094152    0.94339102 </span></span>
-<span><span class="co">##     C3AR1_rna        C3_rna      CD74_rna     CSF1R_rna   HLA-DRA_rna </span></span>
-<span><span class="co">##    0.94277432    0.93651927    0.93628180    0.93554612    0.93182955 </span></span>
-<span><span class="co">##   SIGLEC9_rna    IL10RA_rna    MS4A4A_rna    ADORA3_rna      FGD2_rna </span></span>
-<span><span class="co">##    0.92328733    0.92292107    0.91909216    0.91404692    0.91109604 </span></span>
-<span><span class="co">##    LAPTM5_rna     STAB1_rna       HCK_rna     PTAFR_rna      CD84_rna </span></span>
-<span><span class="co">##    0.90461333    0.90405869    0.90396388    0.90011898    0.89988775 </span></span>
-<span><span class="co">##     CYTH4_rna     MS4A7_rna    SIRPB2_rna     RUNX1_rna    SH3TC1_rna </span></span>
-<span><span class="co">##    0.89827538    0.89250311    0.89203385    0.89173034    0.89082576 </span></span>
-<span><span class="co">##      CD37_rna      IL18_rna    STEAP3_rna       FYB_rna      MSR1_rna </span></span>
-<span><span class="co">##    0.88578012    0.88558732    0.88503274    0.87957245    0.87914404 </span></span>
-<span><span class="co">##      C1QC_rna     DOCK8_rna    CMKLR1_rna     VSIG4_rna      TLR5_rna </span></span>
-<span><span class="co">##    0.87834137    0.87516337    0.87434232    0.87052433    0.86669267 </span></span>
-<span><span class="co">##     TREM2_rna      SCIN_rna      BTG2_rna   SIGLEC8_rna      C1QA_rna </span></span>
-<span><span class="co">##    0.86641949    0.86251896    0.85755337    0.85515538    0.84538301 </span></span>
-<span><span class="co">##     TGFBI_rna    PIK3R5_rna   ADAMTS1_rna    CLEC7A_rna     S1PR3_rna </span></span>
-<span><span class="co">##    0.84536757    0.84233627    0.83583036    0.83423436    0.82535731 </span></span>
-<span><span class="co">##   TMEM119_rna      CTSS_rna     CLIC1_rna      TLR7_rna    IQGAP2_rna </span></span>
-<span><span class="co">##    0.82196903    0.82151641    0.82109966    0.81735518    0.80021262 </span></span>
-<span><span class="co">##      FGL2_rna     KLHL6_rna     LTBP2_rna  SIGLEC10_rna   HLA-DMB_rna </span></span>
-<span><span class="co">##    0.80014392    0.79227627    0.78811550    0.78656997    0.78629965 </span></span>
-<span><span class="co">##    COL8A1_rna      UCP2_rna     CIITA_rna      C1QB_rna    FBLIM1_rna </span></span>
-<span><span class="co">##    0.78532943    0.78043171    0.77845326    0.77178803    0.76323399 </span></span>
-<span><span class="co">##  HLA-DQA1_rna    SLC2A5_rna   ALOX15B_rna   SLC37A2_rna     FKBP5_rna </span></span>
-<span><span class="co">##    0.75994557    0.75408226    0.75017993    0.74853906    0.74461447 </span></span>
-<span><span class="co">##      THBD_rna  HLA-DPA1_rna    SELPLG_rna    RNASE6_rna    MS4A6A_rna </span></span>
-<span><span class="co">##    0.73764817    0.73642525    0.73573903    0.72218947    0.70762774 </span></span>
-<span><span class="co">##      CCR1_rna   FAM129A_rna      CD14_rna        C7_rna      IER3_rna </span></span>
-<span><span class="co">##    0.70440255    0.70378491    0.70233392    0.70213043    0.68454576 </span></span>
-<span><span class="co">##      CD53_rna    S100A4_rna    PDLIM1_rna    GPRC5A_rna     PARVG_rna </span></span>
-<span><span class="co">##    0.67813768    0.67782265    0.67106666    0.66807648    0.66113899 </span></span>
-<span><span class="co">##      SGK1_rna     GPR34_rna     ITGAX_rna     SPHK1_rna  C11orf96_rna </span></span>
-<span><span class="co">##    0.65618938    0.65134262    0.65084388    0.64913399    0.64352477 </span></span>
-<span><span class="co">##    ADAM28_rna    PCDH18_rna    CYP1B1_rna      NGFR_rna     THBS1_rna </span></span>
-<span><span class="co">##    0.63338782    0.62817867    0.62545763    0.62241502    0.61730883 </span></span>
-<span><span class="co">##     F13A1_rna   SIGLEC1_rna    IGFBP4_rna        F5_rna    MS4A14_rna </span></span>
-<span><span class="co">##    0.59992031    0.56682474    0.56215001    0.55344578    0.55266215 </span></span>
-<span><span class="co">##      MRC1_rna     MEDAG_rna VAT1L_protein     SH2D6_rna      APOD_rna </span></span>
-<span><span class="co">##    0.54694702    0.52958781    0.51949931    0.51491910    0.45485914 </span></span>
-<span><span class="co">##     HMOX1_rna     CXCL2_rna PTBP2_protein    AKR1C2_rna ACOT1_protein </span></span>
-<span><span class="co">##    0.45093102    0.42784352    0.38379233    0.36378187    0.32706950 </span></span>
-<span><span class="co">##      MMP9_rna      LIPG_rna     ACKR1_rna </span></span>
-<span><span class="co">##    0.29932805    0.10494025    0.07805484</span></span></code></pre>
+<pre><code><span><span class="co">##    LY6H_protein TBC1D24_protein   RAB12_protein  CSNK1D_protein    PMM1_protein </span></span>
+<span><span class="co">##      1.00000000      0.96067207      0.95018446      0.91373083      0.87930158 </span></span>
+<span><span class="co">##    PDK2_protein LAMTOR1_protein   ARMT1_protein ATP6AP1_protein    EIF1_protein </span></span>
+<span><span class="co">##      0.85923738      0.85679461      0.83362816      0.83116292      0.82305924 </span></span>
+<span><span class="co">##   USP46_protein  PRUNE2_protein   C2CD5_protein    MPC2_protein    SCG2_protein </span></span>
+<span><span class="co">##      0.82070521      0.81406855      0.80837977      0.79741826      0.79489801 </span></span>
+<span><span class="co">##    GMFG_protein   AP1S1_protein   SYNPR_protein    APEH_protein  COL1A1_protein </span></span>
+<span><span class="co">##      0.78972525      0.78775116      0.77560088      0.76911869      0.73923502 </span></span>
+<span><span class="co">##  PRKACA_protein     POR_protein     CPE_protein   TTC7B_protein   HLA-A_protein </span></span>
+<span><span class="co">##      0.72856261      0.72831672      0.71370465      0.70863268      0.69038092 </span></span>
+<span><span class="co">## SNRNP70_protein   SNX32_protein  CAB39L_protein     SYP_protein    GNG5_protein </span></span>
+<span><span class="co">##      0.67340658      0.64531133      0.64488836      0.63591664      0.62045081 </span></span>
+<span><span class="co">## ALDH3A2_protein   SCN3B_protein   EXOC5_protein   SRP54_protein   MAST1_protein </span></span>
+<span><span class="co">##      0.60033147      0.58197165      0.57721314      0.57670350      0.56005774 </span></span>
+<span><span class="co">##   ARMC8_protein   COPG1_protein   WIPI2_protein   TUBG1_protein  GABRA1_protein </span></span>
+<span><span class="co">##      0.54501347      0.53781567      0.53503646      0.52329867      0.51294443 </span></span>
+<span><span class="co">## NECTIN1_protein   ITPR1_protein  SNRPA1_protein GUCY1A2_protein  DLGAP3_protein </span></span>
+<span><span class="co">##      0.45166801      0.44363032      0.41212481      0.39655465      0.36301002 </span></span>
+<span><span class="co">##        C1QB_rna  ATAD3B_protein        CYBB_rna       F13A1_rna        CCR1_rna </span></span>
+<span><span class="co">##      0.26034395      0.24893281      0.22441530      0.17817574      0.13574288 </span></span>
+<span><span class="co">##        CD14_rna        CD53_rna      CX3CR1_rna      LPCAT2_rna        LIPG_rna </span></span>
+<span><span class="co">##      0.12660867      0.11629988      0.10989585      0.08313190      0.05830927 </span></span>
+<span><span class="co">##        PAX8_rna </span></span>
+<span><span class="co">##      0.02647772</span></span></code></pre>
 <ul>
-<li>Top gene in module 4 is SLC1A5_rna</li>
+<li>Top gene in module 4 is LY6H_protein</li>
 <li>TREM2 or CLU, known AD risk genes expressed on microglia are present
 here</li>
 <li>From prior knowledge, many of the genes in module 4 are related to
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diff --git a/docs/articles/demo.html b/docs/articles/demo.html
index 3ed8e36..1a57f04 100644
--- a/docs/articles/demo.html
+++ b/docs/articles/demo.html
@@ -81,7 +81,7 @@ <h1 data-toc-skip>Omix - Sample reports</h1>
                         <h4 data-toc-skip class="author">This vignette
 was created by Eléonore Schneegans and Nurun Fancy</h4>
             
-            <h4 data-toc-skip class="date">29 June, 2023</h4>
+            <h4 data-toc-skip class="date">12 January, 2024</h4>
       
       
       <div class="hidden name"><code>demo.Rmd</code></div>
@@ -102,6 +102,11 @@ <h2 id="single-omic-report-demo">Single omic report demo<a class="anchor" aria-l
 report</a></p>
 </div>
 <div class="section level2">
+<h2 id="pathway-report">Pathway report<a class="anchor" aria-label="anchor" href="#pathway-report"></a>
+</h2>
+<p><a href="../demo/pathway_report.html">Pathway report</a></p>
+</div>
+<div class="section level2">
 <h2 id="multi-omics-report-demo-clustering">Multi-omics report demo (clustering)<a class="anchor" aria-label="anchor" href="#multi-omics-report-demo-clustering"></a>
 </h2>
 <p><a href="../demo/multi_omic_report_Omix_iCluster.html">Multi-omics
diff --git a/docs/authors.html b/docs/authors.html
index 4b9f62e..294fcba 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -75,14 +75,14 @@ <h1 id="citation">Citation</h1>
     </div>
 
 
-    <p>Schneegans E, Fancy N (2023).
+    <p>Schneegans E, Fancy N (2024).
 <em>Omix: A Multi-Omics Integration Pipeline</em>.
 R package version 1.0.0. 
 </p>
     <pre>@Manual{,
   title = {Omix: A Multi-Omics Integration Pipeline},
   author = {Eleonore Schneegans and Nurun Fancy},
-  year = {2023},
+  year = {2024},
   note = {R package version 1.0.0},
 }</pre>
 
diff --git a/docs/index.html b/docs/index.html
index 5ec4baf..0070774 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -81,13 +81,12 @@
 <!-- badges: start -->
 
 <div class="section level2">
-<h2 id="pipeline-overview">Pipeline overview<a class="anchor" aria-label="anchor" href="#pipeline-overview"></a>
+<h2 id="omix-a-transcriptomics-proteomics-integration-pipeline">Omix: A Transcriptomics-Proteomics Integration Pipeline<a class="anchor" aria-label="anchor" href="#omix-a-transcriptomics-proteomics-integration-pipeline"></a>
 </h2>
-<p>The <code>Omix</code> pipeline offers an integration and analysis framework for multi-omics intended to pre-process, analyse, and visualise multimodal data flexibly to address research questions. Omix is built on four consecutive blocks, (1) preparation of the multimodal container, (2) processing and quality control, (3) single omic analyses, and (4) multi-omics vertical integration.</p>
+<p>The <code>Omix</code> pipeline is a specialised framework for pre-processing, analysing, integrating, and visualising bulk transcriptomics and proteomics data. By embedding state of the art bioinformatics tools with novel features into a user-friendly wrapper, Omix streamlines the integrative analysis of bulk transcriptomics and proteomics data, thereby facilitating complex biological investigations, from biomarker discovery to patient stratification.</p>
 <p>Pipeline outputs are standardised and include publication-quality plots, tables, and interactive reports.</p>
-<p><img src="reference/figures/Omix-pipeline.png" width="100%"></p>
-<p>Omix offers a range of state-of-the-art processing functions and integrative models, equipped with versatile parameters and quality control features. This empowers researchers to explore different integration strategies easily, enhancing the speed, scalability, and flexibility of multi-omics analyses.</p>
-<p>While the current version focuses on bulk transcriptomics and proteomics, future iterations aim to encompass a broader range of omics types, expanding the software’s applicability and usefulness.</p>
+<p><img src="reference/figures/Omix-pipeline.jpg" width="100%"></p>
+<p>The Omix pipeline offers an integration and analysis framework for multi-omics intended to pre-process, analyse, and visualise multimodal data flexibly to address research questions. Omix is a wrapper tool built on five consecutive blocks, (1) preparation of the multimodal container, (2) data processing and quality control, (3) single omic analyses, and (4) Transcriptomics-Proteomics vertical integration, (5) Joint Transcriptomics-Proteomics post-integration downstream analyses</p>
 </div>
 <div class="section level2">
 <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
@@ -154,99 +153,6 @@ <h2 id="overview-of-omix-features">Overview of Omix features<a class="anchor" ar
 <p>Omix implements these modular steps and displays results in interactive reports.</p>
 </div>
 <div class="section level2">
-<h2 id="benchmark-of-multi-omics-integration-softwares">Benchmark of multi-omics integration softwares<a class="anchor" aria-label="anchor" href="#benchmark-of-multi-omics-integration-softwares"></a>
-</h2>
-<table class="table">
-<colgroup>
-<col width="3%">
-<col width="11%">
-<col width="5%">
-<col width="7%">
-<col width="15%">
-<col width="4%">
-<col width="32%">
-<col width="9%">
-<col width="3%">
-<col width="8%">
-</colgroup>
-<thead><tr class="header">
-<th align="left">Tool</th>
-<th align="left">Supported omics</th>
-<th align="left">Pre-processing</th>
-<th align="left">Single omic analysis</th>
-<th align="left">Integrative models</th>
-<th align="left">Use case</th>
-<th align="left">Downstream analyses</th>
-<th align="left">Interactive visualisations</th>
-<th align="left">Language</th>
-<th align="left">Ref</th>
-</tr></thead>
-<tbody>
-<tr class="odd">
-<td align="left">Miodin</td>
-<td align="left">SNP, RNA, methylation, Proteins,</td>
-<td align="left">+</td>
-<td align="left">-</td>
-<td align="left">MOFA</td>
-<td align="left">BM</td>
-<td align="left">-</td>
-<td align="left">-</td>
-<td align="left">R</td>
-<td align="left">Ulfenborg, B. (2019).</td>
-</tr>
-<tr class="even">
-<td align="left">MiBiOmics</td>
-<td align="left">miRNA, RNA, Proteins</td>
-<td align="left">-</td>
-<td align="left">-</td>
-<td align="left">Co-inertia analysis</td>
-<td align="left">BD</td>
-<td align="left">Multi-omics networks</td>
-<td align="left">+</td>
-<td align="left">Web</td>
-<td align="left">(Zoppi et al., 2021)</td>
-</tr>
-<tr class="odd">
-<td align="left">Muon</td>
-<td align="left">Single cell omics</td>
-<td align="left">-</td>
-<td align="left">-</td>
-<td align="left">MOFA, WNN</td>
-<td align="left">NA</td>
-<td align="left">-</td>
-<td align="left">-</td>
-<td align="left">Python</td>
-<td align="left">(Bredikhin et al., 2022)</td>
-</tr>
-<tr class="even">
-<td align="left">Movics</td>
-<td align="left">SNP, RNA, methylation, Proteins</td>
-<td align="left">-</td>
-<td align="left">-</td>
-<td align="left">Range of clustering algorithm</td>
-<td align="left">STR</td>
-<td align="left">Survival analysis, enrichment</td>
-<td align="left">-</td>
-<td align="left">R</td>
-<td align="left">(Lu, 2020)</td>
-</tr>
-<tr class="odd">
-<td align="left">Omix</td>
-<td align="left">RNA, Proteins</td>
-<td align="left">+</td>
-<td align="left">+</td>
-<td align="left">MOFA,MEIFESTO, sMBPLS, MBPLS, DIABLO, iCluster</td>
-<td align="left">BD, BM, STR</td>
-<td align="left">Multi-omics signatures, networks, modules, functional/ cell type/ TF enrichment, pseudotime, etc</td>
-<td align="left">+</td>
-<td align="left">R</td>
-<td align="left">NA</td>
-</tr>
-</tbody>
-</table>
-<p>Biomarker Discovery (BD), Biological Mechanisms (BM), Sample stratification (STR)</p>
-</div>
-<div class="section level2">
 <h2 id="getting-started">Getting started<a class="anchor" aria-label="anchor" href="#getting-started"></a>
 </h2>
 <p>The Getting Started section of the documentation contains downloadable examples on how to use Omix.</p>
@@ -260,7 +166,8 @@ <h4 id="datasets">Datasets:<a class="anchor" aria-label="anchor" href="#datasets
 </h4>
 <ul>
 <li>Get started data: syn51533729</li>
-<li>Pseudo-temporal multi-omics integration data: syn51516099</li>
+<li>Pseudo-temporal multi-omics integration data: syn51516099 <a href="https://doi.org/10.7303/syn51516099" class="external-link uri">https://doi.org/10.7303/syn51516099</a>
+</li>
 </ul>
 </div>
 </div>
@@ -278,7 +185,7 @@ <h2 id="docker-image">Docker image<a class="anchor" aria-label="anchor" href="#d
 <h2 id="citation">Citation<a class="anchor" aria-label="anchor" href="#citation"></a>
 </h2>
 <p>Please cite <code>Omix</code> as:</p>
-<p>Eléonore Schneegans, Nurun Fancy, Michael Thomas, Nanet Willumsen, Paul M Matthews, Johanna Jackson (2023) Omix: A Multi-Omics Integration Pipeline</p>
+<p>Eléonore Schneegans, Nurun Fancy, Michael Thomas, Nanet Willumsen, Paul M Matthews, Johanna Jackson (2023) Omix: A Transcriptomics-Proteomics Integration Pipeline</p>
 </div>
 <div class="section level2">
 <h2 id="contributing">Contributing<a class="anchor" aria-label="anchor" href="#contributing"></a>
diff --git a/docs/reference/Transcription_Factor_enrichment.html b/docs/reference/Transcription_Factor_enrichment.html
index da532e4..45b65e0 100644
--- a/docs/reference/Transcription_Factor_enrichment.html
+++ b/docs/reference/Transcription_Factor_enrichment.html
@@ -67,7 +67,7 @@ <h1>Transcription factor target enrichment test</h1>
 <span>  <span class="va">communities</span>,</span>
 <span>  <span class="va">weights</span>,</span>
 <span>  TF_gmt <span class="op">=</span> <span class="st">"Enrichr_Queries.gmt"</span>,</span>
-<span>  threshold <span class="op">=</span> <span class="fl">0.2</span>,</span>
+<span>  threshold <span class="op">=</span> <span class="fl">1.5</span>,</span>
 <span>  direction <span class="op">=</span> <span class="st">"negative"</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
diff --git a/docs/reference/circular_corrplot.html b/docs/reference/circular_corrplot.html
index 690bee0..9db2039 100644
--- a/docs/reference/circular_corrplot.html
+++ b/docs/reference/circular_corrplot.html
@@ -106,6 +106,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/communities_network.html b/docs/reference/communities_network.html
index f0cc2fb..dc72ef9 100644
--- a/docs/reference/communities_network.html
+++ b/docs/reference/communities_network.html
@@ -102,6 +102,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/community_graph.html b/docs/reference/community_graph.html
index f11004d..25c1595 100644
--- a/docs/reference/community_graph.html
+++ b/docs/reference/community_graph.html
@@ -105,6 +105,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/correlation_heatmap.html b/docs/reference/correlation_heatmap.html
index 77195c2..bdb9cc1 100644
--- a/docs/reference/correlation_heatmap.html
+++ b/docs/reference/correlation_heatmap.html
@@ -101,6 +101,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/correlation_heatmap_clusters.html b/docs/reference/correlation_heatmap_clusters.html
index 1832387..8c1f728 100644
--- a/docs/reference/correlation_heatmap_clusters.html
+++ b/docs/reference/correlation_heatmap_clusters.html
@@ -106,6 +106,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/correlation_heatmap_supervised.html b/docs/reference/correlation_heatmap_supervised.html
index a747137..664e294 100644
--- a/docs/reference/correlation_heatmap_supervised.html
+++ b/docs/reference/correlation_heatmap_supervised.html
@@ -106,6 +106,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/extract_weigths.html b/docs/reference/extract_weigths.html
index aa491cd..8f61ca4 100644
--- a/docs/reference/extract_weigths.html
+++ b/docs/reference/extract_weigths.html
@@ -71,7 +71,7 @@ <h1>Extract_weigths from MOFA model for a given factor of interest at a
     <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">extract_weigths</span><span class="op">(</span></span>
 <span>  <span class="va">model</span>,</span>
 <span>  factor <span class="op">=</span> <span class="fl">1</span>,</span>
-<span>  threshold <span class="op">=</span> <span class="fl">0.3</span>,</span>
+<span>  threshold <span class="op">=</span> <span class="fl">1.5</span>,</span>
 <span>  sense_check_variable <span class="op">=</span> <span class="cn">NULL</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
@@ -88,7 +88,7 @@ <h2>Arguments</h2>
 
 
 <dt>threshold</dt>
-<dd><p>Absolute threshold to filter weights</p></dd>
+<dd><p>Number of standard deviation away from the mean weight</p></dd>
 
 
 <dt>sense_check_variable</dt>
diff --git a/docs/reference/figures/Omix-pipeline.jpg b/docs/reference/figures/Omix-pipeline.jpg
new file mode 100644
index 0000000..84d2695
Binary files /dev/null and b/docs/reference/figures/Omix-pipeline.jpg differ
diff --git a/docs/reference/figures/Omix-pipelineold.png b/docs/reference/figures/Omix-pipelineold.png
new file mode 100644
index 0000000..4f17d25
Binary files /dev/null and b/docs/reference/figures/Omix-pipelineold.png differ
diff --git a/docs/reference/getStdiz.html b/docs/reference/getStdiz.html
index e48dd54..21213ba 100644
--- a/docs/reference/getStdiz.html
+++ b/docs/reference/getStdiz.html
@@ -117,6 +117,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 6e3e0d6..702e4d5 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -331,6 +331,10 @@ <h2 id="plotting-functions">Plotting functions <a href="#plotting-functions" cla
           <p><code><a href="plot_optimal_cluster.html">plot_optimal_cluster()</a></code> </p>
         </td>
         <td><p>plot_optimal_cluster</p></td>
+      </tr><tr><td>
+          <p><code><a href="visualise_pathway.html">visualise_pathway()</a></code> </p>
+        </td>
+        <td><p>visualise_pathway</p></td>
       </tr><tr><td>
           <p><code><a href="volcano_interactive.html">volcano_interactive()</a></code> </p>
         </td>
@@ -383,6 +387,14 @@ <h2 id="generate-report-functions">Generate report functions <a href="#generate-
           <p><code><a href="multi_omics_qc.html">multi_omics_qc()</a></code> </p>
         </td>
         <td><p>Generate multi-omics QC results</p></td>
+      </tr><tr><td>
+          <p><code><a href="pathway_report.html">pathway_report()</a></code> </p>
+        </td>
+        <td><p>Generate a report for single omic analysis</p></td>
+      </tr><tr><td>
+          <p><code><a href="proteomics_report.html">proteomics_report()</a></code> </p>
+        </td>
+        <td><p>Generate a report for single omic analysis</p></td>
       </tr><tr><td>
           <p><code><a href="qc_report.html">qc_report()</a></code> </p>
         </td>
diff --git a/docs/reference/integrative_results_unsupervised.html b/docs/reference/integrative_results_unsupervised.html
index 331b2e2..c98ab6e 100644
--- a/docs/reference/integrative_results_unsupervised.html
+++ b/docs/reference/integrative_results_unsupervised.html
@@ -69,7 +69,7 @@ <h1>Downstream analysis for integrated multi-omics data</h1>
 <span>  dependent <span class="op">=</span> <span class="st">"diagnosis"</span>,</span>
 <span>  sense_check_variable <span class="op">=</span> <span class="st">"PHF1"</span>,</span>
 <span>  covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"PHF1"</span>, <span class="st">"amyloid"</span>, <span class="st">"AT8"</span><span class="op">)</span>,</span>
-<span>  weights_threshold <span class="op">=</span> <span class="fl">0.2</span>,</span>
+<span>  weights_threshold <span class="op">=</span> <span class="fl">1.5</span>,</span>
 <span>  correlation_threshold <span class="op">=</span> <span class="fl">0.4</span>,</span>
 <span>  community_detection <span class="op">=</span> <span class="st">"leading_eigen"</span>,</span>
 <span>  pseudotime_analysis <span class="op">=</span> <span class="cn">TRUE</span>,</span>
@@ -87,7 +87,7 @@ <h2>Arguments</h2>
 
 
 <dt>integration_model</dt>
-<dd><p>Possible unsupervised integration methods are <code>MOFA</code>,</p></dd>
+<dd><p>Possible unsupervised integration methods are <code>MOFA</code></p></dd>
 
 
 <dt>dependent</dt>
@@ -103,7 +103,7 @@ <h2>Arguments</h2>
 
 
 <dt>weights_threshold</dt>
-<dd><p>weights threshold</p></dd>
+<dd><p>weights threshold (+/- SD from the mean)</p></dd>
 
 
 <dt>correlation_threshold</dt>
diff --git a/docs/reference/interactive_network.html b/docs/reference/interactive_network.html
index 4ae6302..a834258 100644
--- a/docs/reference/interactive_network.html
+++ b/docs/reference/interactive_network.html
@@ -103,6 +103,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/multi_omic_report.html b/docs/reference/multi_omic_report.html
index b2d7c19..a849de4 100644
--- a/docs/reference/multi_omic_report.html
+++ b/docs/reference/multi_omic_report.html
@@ -111,6 +111,8 @@ <h2>Value</h2>
     <h2>See also</h2>
     <div class="dont-index"><p>Other Report: 
 <code><a href="multi_omics_qc.html">multi_omics_qc</a>()</code>,
+<code><a href="pathway_report.html">pathway_report</a>()</code>,
+<code><a href="proteomics_report.html">proteomics_report</a>()</code>,
 <code><a href="qc_report.html">qc_report</a>()</code>,
 <code><a href="single_omic_report.html">single_omic_report</a>()</code></p></div>
     </div>
diff --git a/docs/reference/multi_omics_qc.html b/docs/reference/multi_omics_qc.html
index c026438..2269093 100644
--- a/docs/reference/multi_omics_qc.html
+++ b/docs/reference/multi_omics_qc.html
@@ -83,6 +83,8 @@ <h2>Value</h2>
     <h2>See also</h2>
     <div class="dont-index"><p>Other Report: 
 <code><a href="multi_omic_report.html">multi_omic_report</a>()</code>,
+<code><a href="pathway_report.html">pathway_report</a>()</code>,
+<code><a href="proteomics_report.html">proteomics_report</a>()</code>,
 <code><a href="qc_report.html">qc_report</a>()</code>,
 <code><a href="single_omic_report.html">single_omic_report</a>()</code></p></div>
     </div>
diff --git a/docs/reference/multiomics_heatmap.html b/docs/reference/multiomics_heatmap.html
index c7a0f15..5037acb 100644
--- a/docs/reference/multiomics_heatmap.html
+++ b/docs/reference/multiomics_heatmap.html
@@ -142,6 +142,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/pathway_report.html b/docs/reference/pathway_report.html
new file mode 100644
index 0000000..5b96b0c
--- /dev/null
+++ b/docs/reference/pathway_report.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Generate a report for single omic analysis — pathway_report • Omix</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Generate a report for single omic analysis — pathway_report"><meta property="og:description" content="Generate a report for single omic analysis"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-reference-topic">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">Omix</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.0.0</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
+     
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+  </a>
+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="../articles/Omix_vignette_CV_MTG.html">Omix - Get started</a>
+    </li>
+    <li>
+      <a href="../articles/Omix_vignette_MAP_CV_pseudotemporal.html">Omix - Pseudotemporal multi-omics integration</a>
+    </li>
+    <li>
+      <a href="../articles/demo.html">Omix - Sample reports</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Generate a report for single omic analysis</h1>
+    
+    <div class="hidden name"><code>pathway_report.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Generate a report for single omic analysis</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">pathway_report</span><span class="op">(</span></span>
+<span>  <span class="va">pathways</span>,</span>
+<span>  report_folder_path <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/getwd.html" class="external-link">getwd</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  report_file <span class="op">=</span> <span class="st">"single_omic_report_Omix"</span>,</span>
+<span>  database <span class="op">=</span> <span class="st">"Reactome_2016"</span>,</span>
+<span>  num_path <span class="op">=</span> <span class="fl">20</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>pathways</dt>
+<dd><p>list of pathways</p></dd>
+
+
+<dt>report_folder_path</dt>
+<dd><p>report_folder_path folder path to save the report.</p></dd>
+
+
+<dt>report_file</dt>
+<dd><p>filename for report (without an extension).</p></dd>
+
+
+<dt>database</dt>
+<dd><p>Enrichment database <code>GO_Molecular_Function_2021</code>,<code>GO_Cellular_Component_2021</code>,
+<code>GO_Biological_Process_2021</code>, <code>Reactome_2016</code> , <code>KEGG_2021_Human</code> , <code>MSigDB_Hallmark_2020</code></p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>Single omic analyses report html</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p>Other Report: 
+<code><a href="multi_omic_report.html">multi_omic_report</a>()</code>,
+<code><a href="multi_omics_qc.html">multi_omics_qc</a>()</code>,
+<code><a href="proteomics_report.html">proteomics_report</a>()</code>,
+<code><a href="qc_report.html">qc_report</a>()</code>,
+<code><a href="single_omic_report.html">single_omic_report</a>()</code></p></div>
+    </div>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Eleonore Schneegans, Nurun Fancy.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/plot_OpenTarget.html b/docs/reference/plot_OpenTarget.html
index 898eef0..09e6e08 100644
--- a/docs/reference/plot_OpenTarget.html
+++ b/docs/reference/plot_OpenTarget.html
@@ -104,6 +104,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/plot_communities.html b/docs/reference/plot_communities.html
index b911d57..aae49a4 100644
--- a/docs/reference/plot_communities.html
+++ b/docs/reference/plot_communities.html
@@ -98,6 +98,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/plot_components.html b/docs/reference/plot_components.html
index 0ed275b..49a2673 100644
--- a/docs/reference/plot_components.html
+++ b/docs/reference/plot_components.html
@@ -111,6 +111,7 @@ <h2>See also</h2>
 <code><a href="plot_communities.html">plot_communities</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/plot_loadings.html b/docs/reference/plot_loadings.html
index 3139bce..f118651 100644
--- a/docs/reference/plot_loadings.html
+++ b/docs/reference/plot_loadings.html
@@ -116,6 +116,7 @@ <h2>See also</h2>
 <code><a href="plot_communities.html">plot_communities</a>()</code>,
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/plot_optimal_cluster.html b/docs/reference/plot_optimal_cluster.html
index 6c996c7..6231b3e 100644
--- a/docs/reference/plot_optimal_cluster.html
+++ b/docs/reference/plot_optimal_cluster.html
@@ -108,6 +108,7 @@ <h2>See also</h2>
 <code><a href="plot_communities.html">plot_communities</a>()</code>,
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
diff --git a/docs/reference/proteomics_report.html b/docs/reference/proteomics_report.html
new file mode 100644
index 0000000..8dc3fd3
--- /dev/null
+++ b/docs/reference/proteomics_report.html
@@ -0,0 +1,143 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Generate a report for single omic analysis — proteomics_report • Omix</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Generate a report for single omic analysis — proteomics_report"><meta property="og:description" content="Generate a report for single omic analysis"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-reference-topic">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">Omix</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.0.0</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="../articles/Omix_vignette_CV_MTG.html">Omix - Get started</a>
+    </li>
+    <li>
+      <a href="../articles/Omix_vignette_MAP_CV_pseudotemporal.html">Omix - Pseudotemporal multi-omics integration</a>
+    </li>
+    <li>
+      <a href="../articles/demo.html">Omix - Sample reports</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Generate a report for single omic analysis</h1>
+    
+    <div class="hidden name"><code>proteomics_report.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Generate a report for single omic analysis</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">proteomics_report</span><span class="op">(</span></span>
+<span>  <span class="va">multiassay</span>,</span>
+<span>  report_folder_path <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/getwd.html" class="external-link">getwd</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  report_file <span class="op">=</span> <span class="st">"single_omic_report_Omix"</span>,</span>
+<span>  slot <span class="op">=</span> <span class="st">"ADvsControl"</span>,</span>
+<span>  database <span class="op">=</span> <span class="st">"Reactome_2016"</span>,</span>
+<span>  num_path <span class="op">=</span> <span class="fl">20</span>,</span>
+<span>  clinical_covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"PHF1"</span>, <span class="st">"amyloid"</span>, <span class="st">"PMD"</span><span class="op">)</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>multiassay</dt>
+<dd><p>Multiassay experiment object generated by Omix</p></dd>
+
+
+<dt>report_folder_path</dt>
+<dd><p>report_folder_path folder path to save the report.</p></dd>
+
+
+<dt>report_file</dt>
+<dd><p>filename for report (without an extension).</p></dd>
+
+
+<dt>slot</dt>
+<dd><p>Slot of interest</p></dd>
+
+
+<dt>database</dt>
+<dd><p>Enrichment database <code>GO_Molecular_Function_2021</code>,<code>GO_Cellular_Component_2021</code>,
+<code>GO_Biological_Process_2021</code>, <code>Reactome_2016</code> , <code>KEGG_2021_Human</code> , <code>MSigDB_Hallmark_2020</code></p></dd>
+
+
+<dt>clinical_covariates</dt>
+<dd><p>clinical covariates for table1</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>Single omic analyses report html</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p>Other Report: 
+<code><a href="multi_omic_report.html">multi_omic_report</a>()</code>,
+<code><a href="multi_omics_qc.html">multi_omics_qc</a>()</code>,
+<code><a href="pathway_report.html">pathway_report</a>()</code>,
+<code><a href="qc_report.html">qc_report</a>()</code>,
+<code><a href="single_omic_report.html">single_omic_report</a>()</code></p></div>
+    </div>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Eleonore Schneegans, Nurun Fancy.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/qc_report.html b/docs/reference/qc_report.html
index e068b66..a047341 100644
--- a/docs/reference/qc_report.html
+++ b/docs/reference/qc_report.html
@@ -112,6 +112,8 @@ <h2>See also</h2>
     <div class="dont-index"><p>Other Report: 
 <code><a href="multi_omic_report.html">multi_omic_report</a>()</code>,
 <code><a href="multi_omics_qc.html">multi_omics_qc</a>()</code>,
+<code><a href="pathway_report.html">pathway_report</a>()</code>,
+<code><a href="proteomics_report.html">proteomics_report</a>()</code>,
 <code><a href="single_omic_report.html">single_omic_report</a>()</code></p></div>
     </div>
 
diff --git a/docs/reference/single_omic_report.html b/docs/reference/single_omic_report.html
index 7146604..b768387 100644
--- a/docs/reference/single_omic_report.html
+++ b/docs/reference/single_omic_report.html
@@ -111,6 +111,8 @@ <h2>See also</h2>
     <div class="dont-index"><p>Other Report: 
 <code><a href="multi_omic_report.html">multi_omic_report</a>()</code>,
 <code><a href="multi_omics_qc.html">multi_omics_qc</a>()</code>,
+<code><a href="pathway_report.html">pathway_report</a>()</code>,
+<code><a href="proteomics_report.html">proteomics_report</a>()</code>,
 <code><a href="qc_report.html">qc_report</a>()</code></p></div>
     </div>
 
diff --git a/docs/reference/spls_wrapper.html b/docs/reference/spls_wrapper.html
index 364dbf1..602070f 100644
--- a/docs/reference/spls_wrapper.html
+++ b/docs/reference/spls_wrapper.html
@@ -81,6 +81,18 @@ <h2>Arguments</h2>
 <dt>dependent</dt>
 <dd><p>Continuous dependent variable for sparse partial least squares</p></dd>
 
+
+<dt>ncomp</dt>
+<dd><p>number of components</p></dd>
+
+
+<dt>test.keepX_rna</dt>
+<dd><p>numeric vector for the different number of variables to test from the transcriptomic dataset</p></dd>
+
+
+<dt>test.keepX_protein</dt>
+<dd><p>numeric vector for the different number of variables to test from proteomic dataset</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
diff --git a/docs/reference/visualise_pathway.html b/docs/reference/visualise_pathway.html
new file mode 100644
index 0000000..4e17945
--- /dev/null
+++ b/docs/reference/visualise_pathway.html
@@ -0,0 +1,135 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>visualise_pathway — visualise_pathway • Omix</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="visualise_pathway — visualise_pathway"><meta property="og:description" content="visualise_pathway"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-reference-topic">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">Omix</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.0.0</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="../articles/Omix_vignette_CV_MTG.html">Omix - Get started</a>
+    </li>
+    <li>
+      <a href="../articles/Omix_vignette_MAP_CV_pseudotemporal.html">Omix - Pseudotemporal multi-omics integration</a>
+    </li>
+    <li>
+      <a href="../articles/demo.html">Omix - Sample reports</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>visualise_pathway</h1>
+    
+    <div class="hidden name"><code>visualise_pathway.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>visualise_pathway</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">visualise_pathway</span><span class="op">(</span><span class="va">pathways</span>, gene_data <span class="op">=</span> <span class="cn">NULL</span>, num_path <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>pathways</dt>
+<dd><p>dataframe of enrichment results</p></dd>
+
+
+<dt>gene_data</dt>
+<dd><p>LogFC</p></dd>
+
+
+<dt>num_path</dt>
+<dd><p>number of pathways to plot</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>viridis</p>
+    </div>
+    <div id="see-also">
+    <h2>See also</h2>
+    <div class="dont-index"><p>Other Plotting: 
+<code><a href="circular_corrplot.html">circular_corrplot</a>()</code>,
+<code><a href="communities_network.html">communities_network</a>()</code>,
+<code><a href="community_graph.html">community_graph</a>()</code>,
+<code><a href="correlation_heatmap_clusters.html">correlation_heatmap_clusters</a>()</code>,
+<code><a href="correlation_heatmap_supervised.html">correlation_heatmap_supervised</a>()</code>,
+<code><a href="correlation_heatmap.html">correlation_heatmap</a>()</code>,
+<code><a href="getStdiz.html">getStdiz</a>()</code>,
+<code><a href="interactive_network.html">interactive_network</a>()</code>,
+<code><a href="multiomics_heatmap.html">multiomics_heatmap</a>()</code>,
+<code><a href="plot_OpenTarget.html">plot_OpenTarget</a>()</code>,
+<code><a href="plot_communities.html">plot_communities</a>()</code>,
+<code><a href="plot_components.html">plot_components</a>()</code>,
+<code><a href="plot_loadings.html">plot_loadings</a>()</code>,
+<code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
+<code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
+<code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
+<code><a href="volcano_plot_limma.html">volcano_plot_limma</a>()</code></p></div>
+    </div>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Eleonore Schneegans, Nurun Fancy.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/volcano_interactive.html b/docs/reference/volcano_interactive.html
index c720c65..2e17e2d 100644
--- a/docs/reference/volcano_interactive.html
+++ b/docs/reference/volcano_interactive.html
@@ -104,6 +104,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
 <code><a href="volcano_plot_limma.html">volcano_plot_limma</a>()</code></p></div>
diff --git a/docs/reference/volcano_interactive_comparison.html b/docs/reference/volcano_interactive_comparison.html
index ab1dc83..bd0d20f 100644
--- a/docs/reference/volcano_interactive_comparison.html
+++ b/docs/reference/volcano_interactive_comparison.html
@@ -96,6 +96,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code>,
 <code><a href="volcano_plot_limma.html">volcano_plot_limma</a>()</code></p></div>
diff --git a/docs/reference/volcano_plot_deseq.html b/docs/reference/volcano_plot_deseq.html
index a09db8a..b499b2f 100644
--- a/docs/reference/volcano_plot_deseq.html
+++ b/docs/reference/volcano_plot_deseq.html
@@ -103,6 +103,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_limma.html">volcano_plot_limma</a>()</code></p></div>
diff --git a/docs/reference/volcano_plot_limma.html b/docs/reference/volcano_plot_limma.html
index 018d51e..bc59d0e 100644
--- a/docs/reference/volcano_plot_limma.html
+++ b/docs/reference/volcano_plot_limma.html
@@ -103,6 +103,7 @@ <h2>See also</h2>
 <code><a href="plot_components.html">plot_components</a>()</code>,
 <code><a href="plot_loadings.html">plot_loadings</a>()</code>,
 <code><a href="plot_optimal_cluster.html">plot_optimal_cluster</a>()</code>,
+<code><a href="visualise_pathway.html">visualise_pathway</a>()</code>,
 <code><a href="volcano_interactive_comparison.html">volcano_interactive_comparison</a>()</code>,
 <code><a href="volcano_interactive.html">volcano_interactive</a>()</code>,
 <code><a href="volcano_plot_deseq.html">volcano_plot_deseq</a>()</code></p></div>
diff --git a/vignettes/.build.timestamp b/vignettes/.build.timestamp
new file mode 100644
index 0000000..e69de29
diff --git a/vignettes/Omix_vignette_MAP_CV_pseudotemporal.Rmd b/vignettes/Omix_vignette_MAP_CV_pseudotemporal.Rmd
index cf3353c..98b3ece 100644
--- a/vignettes/Omix_vignette_MAP_CV_pseudotemporal.Rmd
+++ b/vignettes/Omix_vignette_MAP_CV_pseudotemporal.Rmd
@@ -289,6 +289,7 @@ multiomics_object=vertical_integration(multiassay=multiomics_object,
                                 most_variable_feature=TRUE)
 ```
 
+
 The integration process is successful and all integration related object are stored in the `integration` slot of the multi-omics object.
 
 ```{r}