# Questions about hclust2 output

**URL:** <https://forum.biobakery.org/t/questions-about-hclust2-output/804>\
**Category:** MetaPhlAn\
**Created:** [July 31, 2020, 8:24pm UTC](https://forum.biobakery.org/t/questions-about-hclust2-output/804 "2020-07-31T20:24:18Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![elhenawy](https://avatars.discourse-cdn.com/v4/letter/e/51bf81/32.png) [@elhenawy](https://forum.biobakery.org/u/elhenawy)\
**Post date:** [July 31, 2020, 8:24pm UTC](https://forum.biobakery.org/t/questions-about-hclust2-output/804/1 "2020-07-31T20:24:18Z")

</div>

Question1: How can I adjust the labeling size of the heatmap legend (the one showing the range of values plotted on the top left corner of the png file). The font is too big causing the numbers to overlap with each other, and with the color legend.  
My command is:  
hclust2.py -i merged\_abundance\_table.txt -o merged\_abundance2.png --f\_dist\_f braycurtis --s\_dist\_f braycurtis --cell\_aspect\_ratio 0.5 -l --ftop 50 --fperc 99 --flabel\_size 4 --slabel\_size 4 --max\_flabel\_len 100 --max\_slabel\_len 100 --minv 0.1 --dpi 300 --max\_flabel\_len 100 -c ‘Blues’ --colormap ‘Blues’  
Question2: Are the abundance values scaled by row in hclust2?  
Thanks

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [August 3, 2020, 7:23am UTC](https://forum.biobakery.org/t/questions-about-hclust2-output/804/2 "2020-08-03T07:23:27Z")

</div>

> [@elhenawy](#):
>
> Question1: How can I adjust the labeling size of the heatmap legend (the one showing the range of values plotted on the top left corner of the png file).

You can adjust the font size using the `--colorbar_font_size` parameter.

> [@elhenawy](#):
>
> Question2: Are the abundance values scaled by row in hclust2?

No, scaling is introduced with parameters `-l` or `-s` for log-scale and sqrt-scale, respectively.

---

<div class="post-metadata">

**Author:** ![Dahn-young\_Dong](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/dahn-young_dong/32/1226_2.png) [@Dahn-young\_Dong](https://forum.biobakery.org/u/Dahn-young_Dong)\
**Post date:** [June 30, 2022, 10:59pm UTC](https://forum.biobakery.org/t/questions-about-hclust2-output/804/3 "2022-06-30T22:59:38Z")

</div>

Another question, I am comparing two heatmaps with the same metadata. However, everytime I regenerated the heatmap, the color palette assigned to the metadata categories change. How do I manually specify which color goes with which metadata categories? I have two rows of metadata.

Best

---

<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [July 18, 2022, 10:14am UTC](https://forum.biobakery.org/t/questions-about-hclust2-output/804/4 "2022-07-18T10:14:19Z")

</div>

Hi @Dahn-young_Dong , unfortunately, there is no option in hclust2 to specify the color for each metadata category, it will be chosen randomly