Review updates to figures; core genome analyses

SBRG · Aug 25, 2023 · 71e1157 · 71e1157
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commit 71e1157
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Showing 19 changed files with 12,800 additions and 1,713 deletions.
diff --git a/notebooks/k12_modulome/1b__QC_expression_part2.ipynb b/notebooks/k12_modulome/1b__QC_expression_part2.ipynb
@@ -1588,7 +1588,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.10.10"
   },
   "toc": {
    "base_numbering": 1,

diff --git a/notebooks/k12_modulome/6__summarize_imodulons.ipynb b/notebooks/k12_modulome/6__summarize_imodulons.ipynb
@@ -72,6 +72,26 @@
     "imod_table = ica_data.imodulon_table"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.7026019143235859"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ica_data.imodulon_table['PRECISE-1K_pearson'].median()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/notebooks/k12_modulome/fig__investigate_expression.ipynb b/notebooks/k12_modulome/fig__investigate_expression.ipynb
@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "id": "fb59f5af-35d5-4271-87b9-06d19b5b6bc2",
    "metadata": {},
    "outputs": [],
@@ -55,7 +55,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "id": "3962382f-1d19-4c2f-9903-b616fdd5d0f8",
    "metadata": {},
    "outputs": [],
@@ -68,7 +68,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "id": "6564500b-7fbd-42a9-ae51-57e3ab85bee0",
    "metadata": {},
    "outputs": [],
@@ -81,7 +81,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "id": "f40b09c3-ad8d-4bf2-88a7-57817b1c44c3",
    "metadata": {},
    "outputs": [],
@@ -856,7 +856,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.10.10"
   },
   "toc-showcode": false
  },

diff --git a/notebooks/precise1k/fig__investigate_expression.ipynb b/notebooks/precise1k/fig__investigate_expression.ipynb
diff --git a/notebooks/precise1k/fig__summarize_imodulons.ipynb b/notebooks/precise1k/fig__summarize_imodulons.ipynb
diff --git a/notebooks/precise1k/summarize_imodulons_figs/im_sizes.png b/notebooks/precise1k/summarize_imodulons_figs/im_sizes.png