add subtitles for each conditions

docs/benchmark.md

@@ -22,19 +22,22 @@ We have different alignment options in the pipeline :
 
 Here we have matrices with **4kb** resolution, **normalized to 1** (to the total of reads) and with the **diagonal down to 0**.
 
+#### All chromosomes 4kb, normalized to 1:
 Normal vs iterative             |  Normal vs parasplit   |  Normal vs cutsite
 :-------------------------:|:-------------------------:|:-------------------------:
 ![](images/17.png)  |  ![](images/24.png)   | ![](images/28.png)
 
 We can zoom on a chromosome to better see the details and a **resolution of 1kb**:
 
+#### Chromosome 3 1kb, normalized to 1:
 Normal vs iterative             |  Normal vs parasplit   |  Normal vs cutsite
 :-------------------------:|:-------------------------:|:-------------------------:
 ![](images/chr3_17.png)  |  ![](images/chr3_24.png)   | ![](images/chr3_28.png)
 
 The iterative alignment gives more reads in general but less around the diagonal, in opposite with cutsite and parasplit which give more contacts, especially around the diagonal.
 
-Parasplit vs cutsite             |  Chr3 | Chr3 not normalized
+#### Parasplit vs cutsite
+All chromosomes (4kb, norm to 1)             |  Chromosome 3 (1kb, norm to 1) | Chromosome 3 (1kb, not normalized)
 :-------------------------:|:------------------------:|:------------------------:
 ![](images/104.png)  |  ![](images/chr3_104.png)  | ![](images/chr3_104_noNorm.png)
 
@@ -52,10 +55,12 @@ We have different combinations possible for filtering options :
 
 We are gonna look at the matrices diff for normal alignment, no filtering against each of the other possibilities :
 
+#### All chromosomes (4kb, normalized to 1):
 No filter vs filter             |  No filter vs filter pcr   |  No filter vs both
 :-------------------------:|:-------------------------:|:-------------------------:
 ![](images/21.png)  |  ![](images/30.png)   | ![](images/18.png)
 
+#### Chromosome 3 (1kb, normalized to 1):
 No filter vs filter             |  No filter vs filter pcr   |  No filter vs both
 :-------------------------:|:-------------------------:|:-------------------------:
 ![](images/chr3_21.png)  |  ![](images/chr3_30.png)   | ![](images/chr3_18.png)
@@ -63,7 +68,8 @@ No filter vs filter             |  No filter vs filter pcr   |  No filter vs bot
 We can see a red line around the diagonal for the filtering, and some random adding and losing of contacts for the duplicate filtering. For the combination it doesn't seem different at first look.
 If we look at these matrices without normalization:
 
-No filter vs filter not normalized            |  No filter vs filter pcr not normalized  |  No filter vs both not normalized
+#### Chromosome 3 (1kb, **not** normalized)
+No filter vs filter            |  No filter vs filter pcr  |  No filter vs both
 :-------------------------:|:-------------------------:|:-------------------------:
 ![](images/chr3_21_noNorm.png)  |  ![](images/chr3_30_noNorm.png)   | ![](images/chr3_18_noNorm.png)
 
@@ -72,6 +78,7 @@ The duplicate filtering removes contacts everywhere, we cannot see a pattern and
 
 We can check that the filtering options have the same effect regardless of the mapping situation :
 
+#### Chromosome 3 (1kb, normalized to 1):
 No filter vs filter (iterative)           |  No filter vs filter pcr (iterative)   |  No filter vs both (iterative)
 :-------------------------:|:-------------------------:|:-------------------------:
 ![](images/chr3_42.png)  |  ![](images/chr3_36.png)   | ![](images/chr3_40.png)