reorder figures

aramanlab · Jan 3, 2025 · 614e626 · 614e626
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Showing 11 changed files with 33 additions and 33 deletions.
diff --git a/notebooks/01_figure_01.ipynb → notebooks/01_figure_s01.ipynb b/notebooks/01_figure_01.ipynb → notebooks/01_figure_s01.ipynb
@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "---\n",
-    "title: Fig. 1 - Standard Analyses\n",
+    "title: Fig. S1 - Standard Analyses\n",
     "author: Benjamin Doran\n",
     "date: today\n",
     "---"
@@ -3311,7 +3311,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Fig. S1 - Metabolite variablilty \n",
+    "# Fig. S2 - Metabolite variablilty \n",
     "\n",
     "However, these strains are not functionally identical. Strains of the same species, digest/produce different amounts of metabolite compounds. And it is not simply individual variation. In the plot below we see bi-modal distribution indicating that there are groups of strains that behave differently."
    ]

diff --git a/notebooks/02_figure_02.ipynb → notebooks/02_figure_01.ipynb b/notebooks/02_figure_02.ipynb → notebooks/02_figure_01.ipynb
@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "---\n",
-    "title: Fig. 2 - Defining Spectral Trees\n",
+    "title: Fig. 1 - Defining Spectral Trees\n",
     "author: Benjamin Doran\n",
     "date: today\n",
     "---"
@@ -3271,7 +3271,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Fig. S2 - Local parameter sweep\n",
+    "# Fig. S3 - Local parameter sweep\n",
     "\n",
     "Does spectral inference find the appropriate tree regardless of the number of taxa or number of features?\n",
     "\n",
@@ -4820,7 +4820,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Fig S3 - Understanding SVD math\n",
+    "# Fig. S4 - Understanding SVD math\n",
     "\n",
     "### How similarity and dissimilarity are encoded into spectral components\n",
     "\n",

diff --git a/notebooks/03_figure_03.ipynb → notebooks/03_figure_02.ipynb b/notebooks/03_figure_03.ipynb → notebooks/03_figure_02.ipynb
@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "---\n",
-    "title: Fig. 3 - Convergent evolution example\n",
+    "title: Fig. 2 - Convergent evolution example\n",
     "author: Benjamin Doran\n",
     "date: today\n",
     "---"
@@ -2637,7 +2637,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Fig. S4 - Timing benchmark\n",
+    "# Fig. S5 - Timing benchmark\n",
     "\n",
     "Spectral Inference is fast, it is based on PCA. So it has the potential to scale quite large. Thousands of taxa on a laptop, larger using clusters and distributed computing.\n",
     "\n",

diff --git a/notebooks/04_figure_04.ipynb → notebooks/04_figure_03.ipynb b/notebooks/04_figure_04.ipynb → notebooks/04_figure_03.ipynb
@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "---\n",
-    "title: Fig. 4 - Calculate Spectral Tree\n",
+    "title: Fig. 3 - Calculate Spectral Tree\n",
     "author: Benjamin Doran\n",
     "date: today\n",
     "---"
@@ -31529,7 +31529,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Fig. S5 - Plot GTDB taxonomy on Spectral Tree"
+    "# Fig. S6 - Plot GTDB taxonomy on Spectral Tree"
    ]
   },
   {