8000 T23 fig by t-kimber · Pull Request #235 · volkamerlab/teachopencadd · GitHub
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T23 fig #235

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Merged
merged 3 commits into from
Jun 3, 2022
Merged

T23 fig #235

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517eb1d
Update kinome tree off-target erlotinib
t-kimber Jun 2, 2022
1e78caa
resize figure
t-kimber Jun 2, 2022
f54fa29
Add details to generate kinmap figure
t-kimber Jun 2, 2022
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Binary file modified ...hopencadd/talktorials/T023_what_is_a_kinase/images/kinmap_erlotinib_karaman.png
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12 changes: 10 additions & 2 deletions teachopencadd/talktorials/T023_what_is_a_kinase/talktorial.ipynb
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Expand Up @@ -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"
]
},
{
Expand Down Expand Up @@ -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."
]
},
{
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