update: documentation

ataulhaleem · Jul 4, 2024 · db5c471 · db5c471
1 parent da18bb2
commit db5c471
Show file tree

Hide file tree

Showing 2 changed files with 25 additions and 12 deletions.
diff --git a/pages/modules/Stratification/mds.mdx b/pages/modules/Stratification/mds.mdx
@@ -15,17 +15,25 @@ The MDS analysis is performed using genotype data and the PLINK WebAssembly modu
 The following PLINK command is executed to perform the MDS analysis:
 
 ```bash
-plink --bfile plink --read-genome plink.genome --cluster --K 5 --mds-plot 2 
+plink \
+--bfile plink \
+--read-genome plink.genome \
+--cluster \
+--K 5 \
+--mds-plot 2 
+
+```
 
 Explanation of the flags used
 
---bfile plink: Specifies the base name of the binary fileset (BED, BIM, and FAM files) to be used.
---read-genome plink.genome: Reads the genome file containing pairwise IBS (Identity by State) distance information.
---cluster: Performs clustering on the genotype data.
---K 5: Specifies that the number of clusters (K) to be identified is 5.
---mds-plot 2: Generates a 2-dimensional MDS plot
+| Flag    | value     | Environment     | 
+| :----------------: | :------------:   | :------------   | 
+| --bfile | plink | Specifies the base name of the binary fileset (BED, BIM, and FAM files) to be used. |
+| --read-genome | plink.genome | Reads the genome file containing pairwise IBS (Identity by State) distance information.|
+| --cluster | -- | Performs clustering on the genotype data. |
+| --K | 5 | Specifies that the number of clusters (K) to be identified is 5. |
+| --mds-plot | 2 | Generates a 2-dimensional MDS plot |
 
-```
 ### Visualization
 
 The result of the MDS analysis is a plot that visualizes the genetic distances between samples in two dimensions. The plot below shows five clusters based on IBS distance, highlighting the genetic relationships within the dataset.

diff --git a/pages/modules/Stratification/pca.mdx b/pages/modules/Stratification/pca.mdx
@@ -15,15 +15,20 @@ The PCA analysis is performed using genotype data and PLINK v1.90b7 64-bit (16 J
 The following PLINK command is executed to perform the PCA analysis:
 
 ```bash
-plink --bfile plink --out pca --pca 2
+plink \
+--bfile plink \
+--out pca \
+--pca 2
+```
 
 Explanation of the flags used
 
---bfile plink: Specifies the base name of the binary fileset (BED, BIM, and FAM files) to be used.
---out pca: Specifies the base name for the output files.
---pca 2: Computes the first two principal components for visualization.
+| Flag    | value     | Environment     | 
+| :----------------: | :------------:   | :------------   | 
+| --bfile | plink | Specifies the base name of the binary fileset (BED, BIM, and FAM files) to be used. |
+| --out | pca | Specifies the base name for the output files.|
+| --pca | 2 | Computes the first two principal components for visualization.|
 
-```
 
 ### Visualization
 The PCA plot is visualized using a custom JavaScript component, which colors the points based on their geographic origin. This enhances the interpretability of the plot by allowing users to see how genetic variation correlates with geographic location.