Update 8-pseudobulk-trajectory.ipynb

zktuong · Oct 16, 2023 · 4bf75bd · 4bf75bd
1 parent 591c3e5
commit 4bf75bd
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/docs/notebooks/8-pseudobulk-trajectory.ipynb b/docs/notebooks/8-pseudobulk-trajectory.ipynb
@@ -78,7 +78,7 @@
    "outputs": [],
    "source": [
     "if not os.path.exists(\"demo-pseudobulk.h5ad\"):\n",
-    "    os.system(\"wget ftp://ftp.sanger.ac.uk/pub/users/kp9/demo-pseudobulk.h5ad\")\n"
+    "    os.system(\"wget ftp://ftp.sanger.ac.uk/pub/users/kp9/demo-pseudobulk.h5ad\")"
    ]
   },
   {
@@ -149,7 +149,7 @@
    "outputs": [],
    "source": [
     "adata = sc.read(\"demo-pseudobulk.h5ad\")\n",
-    "adata = ddl.tl.setup_vdj_pseudobulk(adata)\n"
+    "adata = ddl.tl.setup_vdj_pseudobulk(adata)"
    ]
   },
   {
@@ -232,7 +232,7 @@
     }
    ],
    "source": [
-    "pb_adata\n"
+    "pb_adata"
    ]
   },
   {
@@ -275,7 +275,7 @@
    ],
    "source": [
     "sc.tl.pca(pb_adata)\n",
-    "sc.pl.pca(pb_adata, color=\"anno_lvl_2_final_clean\")\n"
+    "sc.pl.pca(pb_adata, color=\"anno_lvl_2_final_clean\")"
    ]
   },
   {
@@ -359,6 +359,7 @@
     "pca_projections = pd.DataFrame(pb_adata.obsm[\"X_pca\"], index=pb_adata.obs_names)\n",
     "dm_res = palantir.utils.run_diffusion_maps(pca_projections, n_components=5)\n",
     "ms_data = palantir.utils.determine_multiscale_space(dm_res)\n",
+    "ms_data.index = ms_data.index.astype(str)\n",
     "\n",
     "pr_res = palantir.core.run_palantir(\n",
     "    ms_data,\n",