Use ArgInfo

notebooks/qc-template.ipynb

@@ -2,19 +2,12 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import tskit\n",
-    "import tszip\n",
-    "\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "import sys\n",
-    "sys.path.append(\"../\")\n",
-    "import sc2ts.utils"
+    "import sc2ts.debug as sd"
    ]
   },
   {
@@ -23,7 +16,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ts = tskit.load(\"../results/XXX.ts\")\n",
+    "ts = tskit.load(\"../results/XX.ts\")\n",
     "ts"
    ]
   },
@@ -33,12 +26,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti = sc2ts.utils.TreeInfo(ts)\n",
-    "\n",
-    "def report(*args, **kwargs):\n",
-    "    display(*ti.node_report(*args, **kwargs))\n",
-    "\n",
-    "ti"
+    "ai = sd.ArgInfo(ts)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ai"
    ]
   },
   {
@@ -54,7 +51,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti.plot_mutations_per_node_distribution()"
+    "ai.plot_mutations_per_node_distribution();"
    ]
   },
   {
@@ -63,7 +60,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti.plot_masked_sites_per_sample()"
+    "ai.plot_mutations_per_site_distribution();"
    ]
   },
   {
@@ -72,7 +69,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti.plot_mutations_per_site_distribution()"
+    "ai.plot_mutations_per_site();"
    ]
   },
   {
@@ -81,7 +78,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti.plot_mutations_per_site()"
+    "ai.plot_ts_tv_per_site();"
    ]
   },
   {
@@ -90,16 +87,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti.plot_masked_samples_per_site()"
+    "ai.plot_mutation_spectrum(min_inheritors=2);"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "ti.plot_diversity()"
+    "# Missing data"
    ]
   },
   {
@@ -108,7 +103,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti.plot_ts_tv_per_site()"
+    "ai.plot_missing_sites_per_sample();"
    ]
   },
   {
@@ -117,7 +112,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti.plot_mutation_spectrum(min_inheritors=2)"
+    "ai.plot_missing_samples_per_site();"
    ]
   },
   {
@@ -133,7 +128,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti.plot_samples_per_day()"
+    "ai.plot_samples_per_day();"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Recombinants"
    ]
   },
   {
@@ -142,14 +144,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ti.plot_recombinants_per_day()"
+    "ai.recombinants_summary()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Pango lineages"
+    "# Branch lengths"
    ]
   },
   {
@@ -158,24 +160,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df_pango = ti.pango_lineages_report()\n",
-    "df_pango"
+    "ai.plot_branch_length_distributions();"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "df_pango_rec = ti.pango_recombinant_lineages_report()\n",
-    "df_pango_rec"
-   ]
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -189,7 +187,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,