From 9f911978923a748280d5ca434b1174c4c8f3faea Mon Sep 17 00:00:00 2001 From: tanliwei Date: Fri, 29 Nov 2024 10:35:13 +0800 Subject: [PATCH] update tutorial. --- docs/build.sh | 2 +- ...iptomic_data_from_the_mouse_midbrain.ipynb | 30 ++++++++++++++++--- 2 files changed, 27 insertions(+), 5 deletions(-) diff --git a/docs/build.sh b/docs/build.sh index a2856a20..bca64cc4 100644 --- a/docs/build.sh +++ b/docs/build.sh @@ -4,4 +4,4 @@ conda activate stereopy-doc rm -rf ./build/* -make html +make html \ No newline at end of file diff --git a/docs/source/Tutorials/Apply_spaTrack_to_infer_cell_transitions_across_multiple_time_points_in_spatial_transcriptomic_data_from_the_mouse_midbrain.ipynb b/docs/source/Tutorials/Apply_spaTrack_to_infer_cell_transitions_across_multiple_time_points_in_spatial_transcriptomic_data_from_the_mouse_midbrain.ipynb index 430c01e9..3c913504 100644 --- a/docs/source/Tutorials/Apply_spaTrack_to_infer_cell_transitions_across_multiple_time_points_in_spatial_transcriptomic_data_from_the_mouse_midbrain.ipynb +++ b/docs/source/Tutorials/Apply_spaTrack_to_infer_cell_transitions_across_multiple_time_points_in_spatial_transcriptomic_data_from_the_mouse_midbrain.ipynb @@ -587,7 +587,15 @@ "id": "e21bafc3-f64a-47b2-a07d-0d58e5388299", "metadata": {}, "source": [ - "## Visualze cell transfer by dynamic figure" + "## Visualze cell transfer by dynamic figure\n", + "\n", + "
\n", + "\n", + "A necessary dependency needs to be installed:\n", + " \n", + " pip install nbformat\n", + "\n", + "
" ] }, { @@ -982,12 +990,25 @@ "source": [ "## Construct gene regulation network\n", "\n", - "Here, we use data from **E12.5** and **E14.5** as an example to construct regulatory network between TF genes and target genes inferred along the developmental trajectory between two time points.TF genes list of Mouse and Human can be download from [the link](http://116.6.21.110:8090/share/3ca60300-e8bd-4d67-8b68-14267e428523)." + "Here, we use data from **E12.5** and **E14.5** as an example to construct regulatory network between TF genes and target genes inferred along the developmental trajectory between two time points.TF genes list of Mouse and Human can be download from [the link](http://116.6.21.110:8090/share/3ca60300-e8bd-4d67-8b68-14267e428523).\n", + "\n", + "\n", + "
\n", + "\n", + "**Torch** is the necessary dependency for this function and needs to be installed first.\n", + "\n", + " CPU: pip install torch==2.4.1+cpu --extra-index-url https://download.pytorch.org/whl\n", + "\n", + " GPU(CUDA11): pip install torch==2.4.1+cu118 --extra-index-url https://download.pytorch.org/whl/\n", + "\n", + " GPU(CUDA12): pip install torch==2.4.1+cu124 --extra-index-url https://download.pytorch.org/whl/\n", + "\n", + "
" ] }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "id": "e8fd4151-9b4f-4be2-a3e8-17fe367669d5", "metadata": { "execution": { @@ -1018,7 +1039,8 @@ " cell_generate_per_time=10000,\n", " cell_select_per_time=50,\n", " training_times=10,\n", - " iter_times=30\n", + " iter_times=30,\n", + " use_gpu=False # set to True to use GPU\n", ")" ] },