9ff765e4c69329fb8f7b0b58066454d70104eff5
chmalee
  Thu Mar 23 10:37:52 2023 -0700
Update gtex cross tissue track description colors, refs #29954

diff --git src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.html src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.html
index d06bcd5..936af2a 100644
--- src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.html
+++ src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.html
@@ -1,143 +1,134 @@
 <h2>
 Description</h2>
 <p>
 This track collection shows data from 
 <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9383269/"
 target="_blank"><em>Single-nucleus cross-tissue molecular reference maps toward
 understanding disease gene function</em></a>. The dataset covers ~200,000 single nuclei
 from a total of 16 human donors across 25 samples, using 4 different sample preparation
 protocols followed by droplet based single-cell RNA-seq. The samples were obtained from
 frozen tissue obtained as part of the Genotype-Tissue Expression (GTEx) project.
 Samples were taken from the esophagus, skeletal muscle, heart, lung, prostate, breast,
 and skin. The dataset includes 43 broad cell classes, some specific to certain tissues
 and some shared across all tissue types.
 </p>
 
 <p>
 There are 2 tracks in this collection. The first track,
 <a href="hgTrackUi?g=atlasCombined" target="_blank">GTEx Atlas Combined Tissue-Cell Type</a>
 allows cells to be grouped together and faceted on up 2 categories: tissue and broad cell type.
 </p>
 
 <p>
 Please see 
 <a href="https://gtexportal.org/home/singleCellOverviewPage" target="_blank">the GTEx portal</a> 
 for further interactive displays and additional data. </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
-Tissue-cell type combinations in the Combined track are colored by which cell type they
-belong to in the below table:
+Tissue-cell type combinations in the Full and Combined tracks are
+colored by which cell type they belong to in the below table:
 <p>
 <table cellpadding='2'>
   <thead>
     <tr>
       <th style="border-bottom: 2px solid;">Color</th>
       <th style="border-bottom: 2px solid;">Cell Type</th>
     </tr>
   </thead>
-  <tr><td style="background-color: rgb(91,57,27);"></td><td>Adipocyte</td></tr>
-  <tr><td style="background-color: rgb(92,138,73);"></td><td>Endothelial cell (lymphatic)</td></tr>
-  <tr><td style="background-color: rgb(47,64,32);"></td><td>Endothelial cell (vascular)</td></tr>
-  <tr><td style="background-color: rgb(240,142,60);"></td><td>Epithelial cell (Hillock)</td></tr>
-  <tr><td style="background-color: rgb(196,170,153);"></td><td>Epithelial cell (alveolar type I)</td></tr>
-  <tr><td style="background-color: rgb(182,50,47);"></td><td>Epithelial cell (alveolar type II)</td></tr>
-  <tr><td style="background-color: rgb(233,148,134);"></td><td>Epithelial cell (basal keratinocyte)</td></tr>
-  <tr><td style="background-color: rgb(222,88,50);"></td><td>Epithelial cell (basal)</td></tr>
-  <tr><td style="background-color: rgb(243,203,72);"></td><td>Epithelial cell (ciliated)</td></tr>
-  <tr><td style="background-color: rgb(188,160,118);"></td><td>Epithelial cell (club)</td></tr>
-  <tr><td style="background-color: rgb(123,79,36);"></td><td>Epithelial cell (cornified keratinocyte)</td></tr>
-  <tr><td style="background-color: rgb(192,120,48);"></td><td>Epithelial cell (luminal)</td></tr>
-  <tr><td style="background-color: rgb(242,192,152);"></td><td>Epithelial cell (mature keratinocyte)</td></tr>
-  <tr><td style="background-color: rgb(188,158,70);"></td><td>Epithelial cell (squamous)</td></tr>
-  <tr><td style="background-color: rgb(240,220,203);"></td><td>Epithelial cell (suprabasal keratinocyte)</td></tr>
-  <tr><td style="background-color: rgb(132,94,87);"></td><td>Epithelial cell (suprabasal)</td></tr>
-  <tr><td style="background-color: rgb(63,41,120);"></td><td>Fibroblast</td></tr>
-  <tr><td style="background-color: rgb(246,245,159);"></td><td>ICCs</td></tr>
-  <tr><td style="background-color: rgb(54,125,118);"></td><td>Immune (B cell)</td></tr>
-  <tr><td style="background-color: rgb(73,164,154);"></td><td>Immune (DC)</td></tr>
-  <tr><td style="background-color: rgb(123,197,203);"></td><td>Immune (DC/macrophage)</td></tr>
-  <tr><td style="background-color: rgb(121,197,205);"></td><td>Immune (Langerhans)</td></tr>
-  <tr><td style="background-color: rgb(79,131,166);"></td><td>Immune (NK cell)</td></tr>
-  <tr><td style="background-color: rgb(148,179,202);"></td><td>Immune (T cell)</td></tr>
-  <tr><td style="background-color: rgb(33,84,118);"></td><td>Immune (alveolar macrophage)</td></tr>
-  <tr><td style="background-color: rgb(207,234,249);"></td><td>Immune (mast cell)</td></tr>
-  <tr><td style="background-color: rgb(0,0,0);"></td><td>Melanocyte</td></tr>
-  <tr><td style="background-color: rgb(149,149,149);"></td><td>Mucous cell</td></tr>
-  <tr><td style="background-color: rgb(160,50,132);"></td><td>Myocyte (NMJ-rich)</td></tr>
-  <tr><td style="background-color: rgb(187,146,185);"></td><td>Myocyte (cardiac)</td></tr>
-  <tr><td style="background-color: rgb(93,76,153);"></td><td>Myocyte (cardiac, cytoplasmic)</td></tr>
-  <tr><td style="background-color: rgb(215,86,148);"></td><td>Myocyte (sk. muscle)</td></tr>
-  <tr><td style="background-color: rgb(229,153,188);"></td><td>Myocyte (sk. muscle, cytoplasmic)</td></tr>
-  <tr><td style="background-color: rgb(218,204,225);"></td><td>Myocyte (smooth muscle)</td></tr>
-  <tr><td style="background-color: rgb(211,129,85);"></td><td>Myoepithelial (basal)</td></tr>
-  <tr><td style="background-color: rgb(155,166,105);"></td><td>Myofibroblast</td></tr>
-  <tr><td style="background-color: rgb(150,192,147);"></td><td>Neuroendocrine</td></tr>
-  <tr><td style="background-color: rgb(99,141,65);"></td><td>Neuronal</td></tr>
-  <tr><td style="background-color: rgb(104,121,83);"></td><td>Pericyte/SMC</td></tr>
-  <tr><td style="background-color: rgb(211,224,147);"></td><td>Satellite cell</td></tr>
-  <tr><td style="background-color: rgb(89,194,59);"></td><td>Schwann cell</td></tr>
-  <tr><td style="background-color: rgb(184,83,88);"></td><td>Sebaceous gland cell</td></tr>
-  <tr><td style="background-color: rgb(138,62,66);"></td><td>Sweat gland cell</td></tr>
-  <tr><td style="background-color: rgb(249,249,249);"></td><td>Unknown</td></tr>
+  <tr><td style="background-color: #00ff00;"></td><td>Endothelial</td></tr>
+  <tr><td style="background-color: #0000ff;"></td><td>Epithelial</td></tr>
+  <tr><td style="background-color: #00d000;"></td><td>Glia</td></tr>
+  <tr><td style="background-color: #ff0000;"></td><td>Immune</td></tr>
+  <tr><td style="background-color: #ffee00;"></td><td>Neuron</td></tr>
+  <tr><td style="background-color: #cc00cc;"></td><td>Stromal</td></tr>
+  <tr><td style="background-color: #888888;"></td><td>Other</td></tr>
+</table>
+</p>
+
+<p>
+Tissue-cell type combinations in the Immune Atlas track are shaded according
+to the below table:
+<table cellpadding='2'>
+  <thead>
+    <tr>
+      <th style="border-bottom: 2px solid;">Color</th>
+      <th style="border-bottom: 2px solid;">Cell Type</th>
+    </tr>
+  </thead>
+  <tr><td style="background-color: rgb(192,173,208);"></td><td>Inflammatory Macrophage</td></tr>
+  <tr><td style="background-color: rgb(47,101,149);"></td><td>Lung Macrophage</td></tr>
+  <tr><td style="background-color: rgb(225,133,52);"></td><td>Monocyte/Macrophage FCGR3A High</td></tr>
+  <tr><td style="background-color: rgb(83,151,67);"></td><td>Monocyte/Macrophage FCGR3A Low</td></tr>
+  <tr><td style="background-color: rgb(180,197,221);"></td><td>Macrophage HLAII High</td></tr>
+  <tr><td style="background-color: rgb(238,165,160);"></td><td>Macrophage LYVE1 High</td></tr>
+  <tr><td style="background-color: rgb(134,105,180);"></td><td>Proliferating Macrophage</td></tr>
+  <tr><td style="background-color: rgb(126,96,87);"></td><td>Dendritic Cell 1</td></tr>
+  <tr><td style="background-color: rgb(181,160,151);"></td><td>Dendritic Cell 2</td></tr>
+  <tr><td style="background-color: rgb(240,189,206);"></td><td>Mature Dendritic Cell</td></tr>
+  <tr><td style="background-color: rgb(199,133,179);"></td><td>Langerhans</td></tr>
+  <tr><td style="background-color: rgb(172,215,165);"></td><td>CD14+ Monocyte</td></tr>
+  <tr><td style="background-color: rgb(188,49,44);"></td><td>CD16+ Monocyte</td></tr>
+  <tr><td style="background-color: rgb(242,196,146);"></td><td>LAM-like</td></tr>
+  <tr><td style="background-color: #888888;"></td><td>Other</td></tr>
 </table>
 </p>
 
 <h2>Methods</h2>
 <p>
 Using the previously collected tissue samples from the Genotype-Tissue Expression
 project, nuclei were isolated using four different protocols and sequenced
 using droplet based single cell RNA-seq. CellBender v2.1 and other standard quality
 control techniques were applied, resulting in 209,126 nuclei profiles across eight
 tissues, with a mean of 918 genes and 1519 transcripts per profile.
 </p>
 
 <p>
 Data from all samples was integrated with a conditional variation autoencoder
 in order to correct for multiple sources of variation like sex, and protocol
 while preserving tissue and cell type specific effects.
 </p>
 
 <p>
 For detailed methods, please refer to Eraslan <em>et al</em>, or the
 <a href="https://gtexportal.org/home/datasets">
 GTEx portal</a> website.
 </p>
 
 <h3>UCSC Methods</h3>
 <p>
 The gene expression files were downloaded from the
 <a href="https://gtexportal.org/home/datasets">
 GTEx portal</a>. The UCSC command line utilities <code>matrixClusterColumns</code>,
 <code>matrixToBarChartBed</code>, and <code>bedToBigBed</code> were used to transform
 these into a bar chart format bigBed file that can be visualized.
 The UCSC utilities can be found on
 <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads"
 target="_blank">our download server</a>.
 </p>
 
 <h2>Data Access</h2>
 <p>
 The raw <a href="/goldenPath/help/barChart.html">bar chart</a> data can be
 explored interactively with the <a href="../cgi-bin/hgTables">Table
 Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For
 automated analysis, the data may be queried from our <a
 href="/goldenPath/help/api.html">REST API</a>. Please refer to our <a
 href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing
 list archives</a> for questions or our <a
 href="../FAQ/FAQdownloads.html#download36">Data Access FAQ</a> for more
 information.</p>
 
 <h2>Credits</h2>
 <p>Thanks to the GTEx Consortium for creating and analyzing these data.</p>
 
 <h2>References</h2>
 <p>
 Eraslan G, Drokhlyansky E, Anand S, Fiskin E, Subramanian A, Slyper M, Wang J, Van Wittenberghe N,
 Rouhana JM, Waldman J <em>et al</em>.
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/35549429" target="_blank">
 Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function</a>.
 <em>Science</em>. 2022 May 13;376(6594):eabl4290.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35549429" target="_blank">35549429</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9383269/" target="_blank">PMC9383269</a>
 </p>