# LEfSe analysis, plotting negative LDA score (log10)

**URL:** <https://forum.biobakery.org/t/lefse-analysis-plotting-negative-lda-score-log10/1294>\
**Category:** LEfSe\
**Created:** [November 17, 2020, 2:57am UTC](https://forum.biobakery.org/t/lefse-analysis-plotting-negative-lda-score-log10/1294 "2020-11-17T02:57:38Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Shaminur](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/shaminur/32/477_2.png) [@Shaminur](https://forum.biobakery.org/u/Shaminur)\
**Post date:** [November 17, 2020, 2:57am UTC](https://forum.biobakery.org/t/lefse-analysis-plotting-negative-lda-score-log10/1294/1 "2020-11-17T02:57:38Z")

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I want to plot LDA score with negative and positive like ![Capture](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/24a1092648f76bc0d2bc6272d081f50c715221ae.png)

where should I need to change the parameter?

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**Author:** ![Kelsey\_Thompson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kelsey_thompson/32/65_2.png) [@Kelsey\_Thompson](https://forum.biobakery.org/u/Kelsey_Thompson)\
**Post date:** [November 18, 2020, 7:36pm UTC](https://forum.biobakery.org/t/lefse-analysis-plotting-negative-lda-score-log10/1294/2 "2020-11-18T19:36:48Z")

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Hi Shaminur,

I am not really sure what you are asking. Do you have results where you have found negative and positive associations but you are only getting the LEfSe plot in one of those directions? For a standard two-variable factor you should receive a plot like the one you posted (from the plot\_res.py command) if you have both positive and negative associations. I _believe_ if you go up to three factors then it adds a third color and makes everything one direction, but I certainly could be wrong about that.

A similar answer was posted here (with a bit more detail): [LDA score treatment comparison: All treatments in one table or separate table for each treatment?](https://forum.biobakery.org/t/lda-score-treatment-comparison-all-treatments-in-one-table-or-separate-table-for-each-treatment/686)

Best,  
Kelsey

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**Author:** ![adakteen](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/adakteen/32/3574_2.png) [@adakteen](https://forum.biobakery.org/u/adakteen)\
**Post date:** [February 19, 2026, 4:06pm UTC](https://forum.biobakery.org/t/lefse-analysis-plotting-negative-lda-score-log10/1294/3 "2026-02-19T16:06:59Z")

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Log-transform the data and centre at log10(1)