add notebooks

pughlab · Nov 20, 2021 · 938d1c0 · 938d1c0
1 parent 9b9418e
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Showing 40 changed files with 149,380 additions and 2,615 deletions.
diff --git a/notebooks/000_ESTIMATE_regression.ipynb b/notebooks/000_ESTIMATE_regression.ipynb
@@ -29,7 +29,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -40,7 +40,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -50,7 +50,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 4,
    "metadata": {
     "scrolled": true
    },
@@ -342,7 +342,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -369,7 +369,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -394,7 +394,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -404,7 +404,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 8,
    "metadata": {
     "scrolled": true
    },
@@ -438,7 +438,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 246,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -462,16 +462,13 @@
     }
    ],
    "source": [
-    "if(file.exists(paste(plotpath,\"ESTIMATE_simulation_fit.pdf\", sep = \"\"))){\n",
-    "    message(\"file exists!\")\n",
-    "} else{\n",
+    "\n",
     "    pdf(file = paste(plotpath,\"ESTIMATE_simulation_fit.pdf\", sep = \"\"),\n",
     "        width = 10, \n",
     "        height = 10,\n",
     "        useDingbats = FALSE)\n",
     "    print(simplot)\n",
-    "    dev.off()\n",
-    "    }"
+    "    dev.off()\n"
    ]
   },
   {

diff --git a/notebooks/000_IHC_plots.ipynb b/notebooks/000_IHC_plots.ipynb
diff --git a/notebooks/00_Div_validation_plots.ipynb b/notebooks/00_Div_validation_plots.ipynb
diff --git a/notebooks/03_exp_matrix_4ESTIMATE.ipynb b/notebooks/03_exp_matrix_4ESTIMATE.ipynb
@@ -403,6 +403,34 @@
     "head(CBTTCtpm)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "0"
+      ],
+      "text/latex": [
+       "0"
+      ],
+      "text/markdown": [
+       "0"
+      ],
+      "text/plain": [
+       "[1] 0"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "CBTTCtpm[ CBTTCtpm$hgnc_symbol == \"DAZ1\", \"7316-905\"]"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 13,