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My docs update #12

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Updated documentation for Read the Docs
Jul 23, 2024
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Updated documentation for Read the Docs set
Jul 23, 2024
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Update index.md
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Update Combination_Kidney_IgAN.md
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Update Combination_Kidney_IgAN.md
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11 changes: 6 additions & 5 deletions docs/source/Combination_Kidney_IgAN.md
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@@ -1,9 +1,10 @@
### Trajectory Analysis of Kidney IgAN Data with PILOT
### Trajectory Analysis and Integration of Modalities using Kidney IgAN (Pathomics) Data with PILOT

<div class="alert alert-block alert-info">
<b>PILOT</b>

Welcome to the PILOT Package Tutorial for pathomics Data!
With this tutorial, we learn not only how to analyze the Pathomics Data but also how to integrate multimodal data with PILOT.

You can find the pathomics data [here](https://github.com/CostaLab/PILOT/tree/main/Tutorial/Datasets).

Expand All @@ -15,7 +16,7 @@ import pilotpy as pl
import scanpy as sc
```

#### Kidney_IgAN Tubuli
#### Kidney_IgAN Tubuli (first modality)

##### Reading Anndata
<div class="alert alert-block alert-info">
Expand Down Expand Up @@ -93,7 +94,7 @@ pl.pl.trajectory(adata_T, colors = ['red','blue','orange'])



#### Kidney_IgAN Glomeruli
#### Kidney_IgAN Glomeruli (second modality)

##### Reading Anndata
<div class="alert alert-block alert-info">
Expand Down Expand Up @@ -144,9 +145,9 @@ pl.pl.trajectory(adata_G, colors = ['red','blue','orange'])



#### Combination:
#### Integration of modalities:
<div class="alert alert-block alert-info">
Here, we combine the distances of samples. We get the sum of distances of samples based on Tubuli and Glomeruli distances.
Here, we integrate the distances from the first (Tubuli) and second (Glomeruli) modalities. We get the sum of the distances of samples.
</div>


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