Merge pull request #235 from volkamerlab/T23-fig

T23 fig
volkamerlab · Jun 3, 2022 · 7dff391 · 7dff391
2 parents 47e3c32 + f54fa29
commit 7dff391
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diff --git a/...hopencadd/talktorials/T023_what_is_a_kinase/images/kinmap_erlotinib_karaman.png b/...hopencadd/talktorials/T023_what_is_a_kinase/images/kinmap_erlotinib_karaman.png
diff --git a/teachopencadd/talktorials/T023_what_is_a_kinase/talktorial.ipynb b/teachopencadd/talktorials/T023_what_is_a_kinase/talktorial.ipynb
@@ -510,7 +510,11 @@
     "There are some KinMap trees shown in this notebook. The code below generates the KinMap CSV files to be uploaded to KinMap:\n",
     "http://www.kinhub.org/kinmap.\n",
     "\n",
-    "_Note_: PNG downloads do not seem to work anymore, thus download as SVG and convert to PNG in your terminal (Linux) via `convert -density 25 my_kinmap_figure.svg my_kinmap_figure.png` (SVG cannot be included in Jupyter notebooks out-of-the-box)."
+    "_Note_:\n",
+    "1. PNG downloads do not seem to work anymore, thus download as SVG and convert to PNG in your terminal (Linux) via `convert -density 25 my_kinmap_figure.svg my_kinmap_figure.png` (SVG cannot be included in Jupyter notebooks out-of-the-box).\n",
+    "2. If SVG download doesn't render the figure properly, open your favorite text editor and copy paste this into the SVG file: `xmlns:xlink=\"http://www.w3.org/1999/xlink\"`, resulting in something similar to this in the first few lines:\n",
+    "\n",
+    "`<svg id=\"svgCopy\" viewBox=\"0 0 1591 1959\" preserveAspectRatio=\"xMinYMin meet\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" style=\"\"><desc>Created with Snap</desc><defs></defs><g`\n"
    ]
   },
   {
@@ -678,7 +682,11 @@
     "- Select \"Data type\": Karaman et al., 2018\n",
     "- Select \"Karaman et al., 2018\": Erlotinib\n",
     "- Click \"Add source\"\n",
-    "- Click \"Apply\""
+    "- In **settings**, select \"RoyalBlue\" in **Fill**\n",
+    "- Click \"Apply\"\n",
+    "- Click on the speech bubble on the top right of the kinome tree to disable annotations.\n",
+    "\n",
+    "_Note_: the name of the on/off-targets (EGFR, GAK, LOK, SLK) have been added manually."
    ]
   },
   {