Heatmap HTML file downloaded instead of SVG file ?

User Support
1

Hello,

I tried the following command lines to generate a heatmap

qiime taxa collapse
--i-table table.qza
--i-taxonomy taxonomy.qza
--p-level 6
--o-collapsed-table collapsed-table-l6.qza

qiime feature-table heatmap
--i-table
--m-sample-metadata-file
--m-sample-metadata-column Disease
--p-metric correlation
--p-method complete
--o-visualization

“I exported a heatmap from QIIME 2 View, but it downloads only as an HTML file. Right-clicking and saving doesn’t change the format. How can I correctly download the heatmap data in its usable file format?”

2

Hello @M_F,

What version of QIIME 2 are you using on what operating system, and what browser are you using to load QIIME 2 View?

If I generate a heatmap using QIIME 2 Amplicon 2025.7 and click on the "Download SVG" button, it redirects me to a webpage that contains only the SVG. I can then right-click on the page, select "save page as...," and have it download my SVG. I believe the SVG should be downloading automatically when I click the "Download SVG" button instead of redirecting me, but it sounds like what you are describing is that when you click the "Download SVG" button, it begins downloading an HTML file. Is that correct?

Thank you,
Anthony Simard

4

Hello @Oddant1

Thanks for the reply.

I’m using windows as operating system, browser = google chrome to load QIIME 2 VIEW. When i click the "Download SVG" button, it begins downloading an HTML file. When i switched to ubuntu operating system the issue was fixed.

Best

5

That is very strange...

6

Here's a heatmap that I made. Does this cause the same thing to happen?

heatmap_body-site.qzv (2.3 MB)

Here is how I made it:

qiime feature-table heatmap \
  --i-table                30668/table-dada2.qza \
  --m-sample-metadata-file 30668/sample-metadata.tsv \
  --m-sample-metadata-column "body-site" \
  --p-metric correlation \
  --p-method complete \
  --o-visualization.       30668/heatmap_body-site.qzv

P.S. This is the first Qiime2 heatmap that I know of the internet!
I looked for public ones, but could not find any examples. :person_shrugging:

7

I also couldn't find examples. I am unable to reproduce this behavior with that heatmap or one I made.

Did Windows 11 on Edge, Chrome, and Firefox.

8

Here's my best guess

  1. Right clicking on the SVG itself, not the download button,
  2. Save image as...
  3. defaults to .htm

image
image550×457 24.5 KB

EDIT:

it downloads only as an HTML file

That's not the bug Meriem found