# \#heatmap **URL:** https://forum.qiime2.org/tag/heatmap/129.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [Heatmaps- Plugin error from feature-table:](https://forum.qiime2.org/t/heatmaps-plugin-error-from-feature-table/28479)
**Author:** [@sophscutt](https://forum.qiime2.org/u/sophscutt)\ **Replies:** 1\ **Last updated:** [December 1, 2023, 4:07pm UTC](https://forum.qiime2.org/t/heatmaps-plugin-error-from-feature-table/28479 "2023-12-01T16:07:57Z")
Hello, I have some Qiime 2 experience but im really struggling with this. Im trying to create a heatmap of my data. This is the command im using: qiime feature-table heatmap --i-table ep-filtered-table.qza --m-feature… --- ## [Change color scheme](https://forum.qiime2.org/t/change-color-scheme/26730)
**Author:** [@kyasarin](https://forum.qiime2.org/u/kyasarin)\ **Replies:** 1\ **Last updated:** [June 9, 2023, 4:37pm UTC](https://forum.qiime2.org/t/change-color-scheme/26730 "2023-06-09T16:37:07Z")
Hi! Is there a way I can change the arrangement of color? It's quite misleading to see green as the lowest frequency rather than gray. Is it possible to flip the color of this heatmap? Thanks! --- ## [mmvec: strange biplot and heat map results](https://forum.qiime2.org/t/mmvec-strange-biplot-and-heat-map-results/25199)
**Author:** [@LenaFloerl](https://forum.qiime2.org/u/LenaFloerl)\ **Replies:** 3\ **Last updated:** [February 15, 2023, 6:03pm UTC](https://forum.qiime2.org/t/mmvec-strange-biplot-and-heat-map-results/25199 "2023-02-15T18:03:20Z")
Dear :qiime2: community, I am trying to estimate microbe-metabolite interactions with mmvec (in qiime-2020.6 since tensorflow won't install in newer qiime2 versions) and my biplot and heat map look really strange! … --- ## [Building heatmap using Qiime2r](https://forum.qiime2.org/t/building-heatmap-using-qiime2r/25034)
**Author:** [@gcook207](https://forum.qiime2.org/u/gcook207)\ **Replies:** 4\ **Last updated:** [January 24, 2023, 4:47pm UTC](https://forum.qiime2.org/t/building-heatmap-using-qiime2r/25034 "2023-01-24T16:47:48Z")
Hello all! I was wondering if you could help me construct a heat map using qiime2r. I have been using code from some of the other posts on here, but seem to need additional tweaking I cant figure out. Here is the code … --- ## [Heatmap of core microbiome using qiime2R](https://forum.qiime2.org/t/heatmap-of-core-microbiome-using-qiime2r/24351)
**Author:** [@GioFranco](https://forum.qiime2.org/u/GioFranco)\ **Replies:** 1\ **Last updated:** [October 5, 2022, 2:14am UTC](https://forum.qiime2.org/t/heatmap-of-core-microbiome-using-qiime2r/24351 "2022-10-05T02:14:11Z")
Hello, I'm trying to build a heatmap using data that was imported using qiime2R -- I'm not quite sure if this is the place to post this question, but I really don't know how to solve this. -- Please see below: The p… --- ## [Heatmapping Beta diversity](https://forum.qiime2.org/t/heatmapping-beta-diversity/24244)
**Author:** [@Jan\_Kollar](https://forum.qiime2.org/u/Jan_Kollar)\ **Replies:** 2\ **Last updated:** [September 23, 2022, 10:26am UTC](https://forum.qiime2.org/t/heatmapping-beta-diversity/24244 "2022-09-23T10:26:41Z")
Hi all, newcomer to both qiime2 and microbial science here. I'm wondering (and not finding an answer in either qiime2 docs or the forum) whether it's possible in qiime2 to produce a heatmap where both x and y axes repre… --- ## [Qiime2R Heatmap construction challenges](https://forum.qiime2.org/t/qiime2r-heatmap-construction-challenges/24033)
**Author:** [@tafara\_bute](https://forum.qiime2.org/u/tafara_bute)\ **Replies:** 0\ **Last updated:** [August 30, 2022, 8:33pm UTC](https://forum.qiime2.org/t/qiime2r-heatmap-construction-challenges/24033 "2022-08-30T20:33:03Z")
I'm using Qiime2 2022.2. I have been trying to come up with a heat map in qiime2r following a tutorial by @jbisanz. Here is an output . Please help to guide me through, where I could have missed it. Below is the code … --- ## [heatmap reordering samples](https://forum.qiime2.org/t/heatmap-reordering-samples/23760)
**Author:** [@rnasrah](https://forum.qiime2.org/u/rnasrah)\ **Replies:** 1\ **Last updated:** [August 1, 2022, 3:26pm UTC](https://forum.qiime2.org/t/heatmap-reordering-samples/23760 "2022-08-01T15:26:25Z")
Hello, I have created a heatmap of my data where I have reordered my samples based on weight change (my two groups labelled AisGS vs BisLoss) using the following command: qiime feature-table heatmap --i-table table.q… --- ## [Determining core bacteria](https://forum.qiime2.org/t/determining-core-bacteria/22730)
**Author:** [@msyamsulrjl](https://forum.qiime2.org/u/msyamsulrjl)\ **Replies:** 1\ **Last updated:** [April 9, 2022, 6:41pm UTC](https://forum.qiime2.org/t/determining-core-bacteria/22730 "2022-04-09T18:41:06Z")
Hi, i am trying to determining the core bacteria of my samples. as far as i know, we can determine the core bacteria with heatmaps that generate by the different of frequency of occurences from each bacteria in all habit… --- ## [Error when trying to group heatmap](https://forum.qiime2.org/t/error-when-trying-to-group-heatmap/20374)
**Author:** [@paul\_nam](https://forum.qiime2.org/u/paul_nam)\ **Replies:** 1\ **Last updated:** [August 3, 2021, 12:00pm UTC](https://forum.qiime2.org/t/error-when-trying-to-group-heatmap/20374 "2021-08-03T12:00:46Z")
Hi, I think I have same problem as @SetaPark had. But, I don't think I am understanding the suggested solution. I am trying to average my samples by group and visualize the group average using heat map. The heatmap… --- ## [Heatmap - weighted\_unifrac Mantel correlation](https://forum.qiime2.org/t/heatmap-weighted-unifrac-mantel-correlation/19589)
**Author:** [@chiara](https://forum.qiime2.org/u/chiara)\ **Replies:** 2\ **Last updated:** [May 18, 2021, 3:09pm UTC](https://forum.qiime2.org/t/heatmap-weighted-unifrac-mantel-correlation/19589 "2021-05-18T15:09:39Z")
Dear All, thanks in advance for your attention. I am trying to run the beta-rarefaction: Beta diversity rarefaction using the weighted unifrac distance matrix. My doubt is the interpretation of the heatmap weighted un… --- ## [Heatmap metric vs method](https://forum.qiime2.org/t/heatmap-metric-vs-method/18839)
**Author:** [@hsapers](https://forum.qiime2.org/u/hsapers)\ **Replies:** 3\ **Last updated:** [March 12, 2021, 3:46pm UTC](https://forum.qiime2.org/t/heatmap-metric-vs-method/18839 "2021-03-12T15:46:23Z")
Hello - I have what's likely a pretty basic question - but can't seem to find documentation to confirm: I'm running qiime feature-table heatmap (using transformed relative abundance I re-imported as a FeatureTable\[Frequ… --- ## [filter top genera level heatmaps](https://forum.qiime2.org/t/filter-top-genera-level-heatmaps/18814)
**Author:** [@SaraGajas](https://forum.qiime2.org/u/SaraGajas)\ **Replies:** 2\ **Last updated:** [March 11, 2021, 9:21am UTC](https://forum.qiime2.org/t/filter-top-genera-level-heatmaps/18814 "2021-03-11T09:21:01Z")
Hi everyone! I'm having some difficulties creating a heatmap. I created a collapsed table from the merged table at the genus level and I wanted to include the most abundant OTUs. First of all, I tried to filter the col… --- ## [sample classifier results without upper cladogram](https://forum.qiime2.org/t/sample-classifier-results-without-upper-cladogram/17435)
**Author:** [@Pablo\_V](https://forum.qiime2.org/u/Pablo_V)\ **Replies:** 1\ **Last updated:** [November 13, 2020, 2:23pm UTC](https://forum.qiime2.org/t/sample-classifier-results-without-upper-cladogram/17435 "2020-11-13T14:23:46Z")
Hi, I have obtained the results from the sample classifier plug-in. However, I got three questions: (1) Why do I find more features associated with one microbiome than with the other (i.e. Infested vs Healthy)? I am as… --- ## [QIIME plugin error from mmvec](https://forum.qiime2.org/t/qiime-plugin-error-from-mmvec/16690)
**Author:** [@jhaffner09](https://forum.qiime2.org/u/jhaffner09)\ **Replies:** 9\ **Last updated:** [October 22, 2020, 2:14am UTC](https://forum.qiime2.org/t/qiime-plugin-error-from-mmvec/16690 "2020-10-22T02:14:11Z")
Hello, I've been trying to use the emperor plugin to create heatmaps from mmvec using the tutorial posted on github (GitHub - biocore/mmvec: Neural networks for microbe-metabolite interaction analysis). My code is: $ q… --- ## [making sample-ids appear in a specific order in the heatmap](https://forum.qiime2.org/t/making-sample-ids-appear-in-a-specific-order-in-the-heatmap/15710)
**Author:** [@anirban.mcgill](https://forum.qiime2.org/u/anirban.mcgill)\ **Replies:** 4\ **Last updated:** [July 22, 2020, 11:10pm UTC](https://forum.qiime2.org/t/making-sample-ids-appear-in-a-specific-order-in-the-heatmap/15710 "2020-07-22T23:10:06Z")
Hello :smiley: I successfully constructed a heatmap using the feature-table (I was also able to remove redundancy by grouping the metadata tables)-thank you to all the relevant discussions on the forum! I have 2 questi… --- ## [Error during Heatmap Generation](https://forum.qiime2.org/t/error-during-heatmap-generation/14365)
**Author:** [@fhermanto96](https://forum.qiime2.org/u/fhermanto96)\ **Replies:** 5\ **Last updated:** [April 7, 2020, 9:31pm UTC](https://forum.qiime2.org/t/error-during-heatmap-generation/14365 "2020-04-07T21:31:43Z")
Dear expert, I want to create a heatmap for my analysis, but I have an error for it. First I filter my table based on this page: then I filter my table based on the frequency only to obtain desired visualized taxa in … --- ## [Captions beside branches of heatmaps](https://forum.qiime2.org/t/captions-beside-branches-of-heatmaps/13109)
**Author:** [@Sparkle](https://forum.qiime2.org/u/Sparkle)\ **Replies:** 4\ **Last updated:** [February 7, 2020, 4:18pm UTC](https://forum.qiime2.org/t/captions-beside-branches-of-heatmaps/13109 "2020-02-07T16:18:50Z")
Hello! I'm trying to create a heatmap through the plugin qiime gneiss dendrogram-heatmap. It resulted into something similar: However, I'd like to see a sort of 'caption' on the sid… --- ## [how to filter features to view on a heat map?](https://forum.qiime2.org/t/how-to-filter-features-to-view-on-a-heat-map/9338)
**Author:** [@Shruthi](https://forum.qiime2.org/u/Shruthi)\ **Replies:** 4\ **Last updated:** [May 2, 2019, 1:23am UTC](https://forum.qiime2.org/t/how-to-filter-features-to-view-on-a-heat-map/9338 "2019-05-02T01:23:44Z")
Hi, I want to construct a heat map at family level. I have 21 samples in total out of which nine belongs to subject 1 and twelve belongs to subject 2. I am able to generate a heat map but I want to filter out low frequ… --- ## [Error while running feature-table heatmap in 2019.1 version](https://forum.qiime2.org/t/error-while-running-feature-table-heatmap-in-2019-1-version/8738)
**Author:** [@Elise](https://forum.qiime2.org/u/Elise)\ **Replies:** 14\ **Last updated:** [March 19, 2019, 12:51am UTC](https://forum.qiime2.org/t/error-while-running-feature-table-heatmap-in-2019-1-version/8738 "2019-03-19T00:51:56Z")
Hi! I received an error when I used feature-table heatmap: Plugin error from feature-table: negative dimensions are not allowed Log information: qiime2-2019.1) med243121:Eksaserbasjonssekvenseringdata ele010$ cd /U… --- ## [Generate a heatmap using unweighted unifrac distance matrix](https://forum.qiime2.org/t/generate-a-heatmap-using-unweighted-unifrac-distance-matrix/7784)
**Author:** [@Bookworm1225](https://forum.qiime2.org/u/Bookworm1225)\ **Replies:** 2\ **Last updated:** [January 14, 2019, 8:42pm UTC](https://forum.qiime2.org/t/generate-a-heatmap-using-unweighted-unifrac-distance-matrix/7784 "2019-01-14T20:42:16Z")
Hello! I am relatively new to using QIIME 2. I currently use the the 2018.4 version. I recently used the beta rarefaction analysis to produce the jackknifed emperor plot, heatmap, and clustered phylogenetic tree using t… --- ## [RelativeFrequency table heatmap](https://forum.qiime2.org/t/relativefrequency-table-heatmap/7527)
**Author:** [@vheidrich](https://forum.qiime2.org/u/vheidrich)\ **Replies:** 2\ **Last updated:** [January 2, 2019, 6:00pm UTC](https://forum.qiime2.org/t/relativefrequency-table-heatmap/7527 "2019-01-02T18:00:29Z")
Hi, Is there a way to use feature table heatmap function to generate a heatmap representation of a RelativeFrequency feature table? I checked QIIME2 Docs and apparently this function accepts exclusively Frequency type t… --- ## [Heatmap and the legend](https://forum.qiime2.org/t/heatmap-and-the-legend/6682)
**Author:** [@Jo\_mee](https://forum.qiime2.org/u/Jo_mee)\ **Replies:** 3\ **Last updated:** [November 2, 2018, 2:57pm UTC](https://forum.qiime2.org/t/heatmap-and-the-legend/6682 "2018-11-02T14:57:23Z")
Hi everyone, I am trying to personalize the heatmap I have generated using: qiime feature-table heatmap --i-table collapsed-table-lvl7-dada2-LB18\_31\_1-filtered-edited.qza --m-metadata-file metadata-LB18\_31-L1.csv --… --- ## [Abundances of taxa by group](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208)
**Author:** [@alfanon](https://forum.qiime2.org/u/alfanon)\ **Replies:** 6\ **Last updated:** [October 3, 2018, 6:53am UTC](https://forum.qiime2.org/t/abundances-of-taxa-by-group/6208 "2018-10-03T06:53:58Z")
Dear all, I am trying to create a table with the abundances (or relative abundances) of taxa at different taxonomic levels (phylum, family, genus) from my feature table, where the abundances are given not by sample, rat… --- ## [Heatmap using Bray-Curtis dissimilarity dendrogram](https://forum.qiime2.org/t/heatmap-using-bray-curtis-dissimilarity-dendrogram/5211)
**Author:** [@Manuss\_Ponce](https://forum.qiime2.org/u/Manuss_Ponce)\ **Replies:** 2\ **Last updated:** [July 25, 2018, 9:11am UTC](https://forum.qiime2.org/t/heatmap-using-bray-curtis-dissimilarity-dendrogram/5211 "2018-07-25T09:11:04Z")
Hi everyone, I´m trying to perform a heatmap of my 16s feature-table using qiime feature-table heatmap, but I would like to sort the Y axis (samples) based on a Bray-Curtis dissimilarity dendrogram. Is that possible by … --- ## [Cannot open heatmap saved as sgv](https://forum.qiime2.org/t/cannot-open-heatmap-saved-as-sgv/4641)
**Author:** [@alfanon](https://forum.qiime2.org/u/alfanon)\ **Replies:** 5\ **Last updated:** [June 22, 2018, 8:49pm UTC](https://forum.qiime2.org/t/cannot-open-heatmap-saved-as-sgv/4641 "2018-06-22T20:49:54Z")
Hello, I created an heatmap with the command qiime feature-table heatmap. Then I open the qzv file in qiime2 view (online) and click on Download SVG. Another tab is created with the image. In Firefox I save the page as … --- ## [Heat map issues](https://forum.qiime2.org/t/heat-map-issues/3980)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 3\ **Last updated:** [May 1, 2018, 3:36pm UTC](https://forum.qiime2.org/t/heat-map-issues/3980 "2018-05-01T15:36:58Z")
I recently made a heatmap and had a few quick questions about it. Is there a setting where I can put the names of the phylums in alphabetical order? Also, I grouped my samples together by age prior to running the comm… --- ## [Error when trying to group samples together then create heat map](https://forum.qiime2.org/t/error-when-trying-to-group-samples-together-then-create-heat-map/3927)
**Author:** [@Stephanieorch](https://forum.qiime2.org/u/Stephanieorch)\ **Replies:** 6\ **Last updated:** [April 27, 2018, 6:04pm UTC](https://forum.qiime2.org/t/error-when-trying-to-group-samples-together-then-create-heat-map/3927 "2018-04-27T18:04:06Z")
When I run the qiime feature-table group command using qiime feature-table group \\ --i-table "$BIOM.qza" \\ --p-axis "sample" \\ --m-metadata-file "merge.tsv" \\ --m-metadata-column "age" \\ --p-mode "me… --- ## [Feature-table heatmap with no clustering on neither axes](https://forum.qiime2.org/t/feature-table-heatmap-with-no-clustering-on-neither-axes/3826)
**Author:** [@jjmmii](https://forum.qiime2.org/u/jjmmii)\ **Replies:** 1\ **Last updated:** [April 18, 2018, 9:44pm UTC](https://forum.qiime2.org/t/feature-table-heatmap-with-no-clustering-on-neither-axes/3826 "2018-04-18T21:44:45Z")
Occasionally it is useful to compare different heatmaps without clustering on neither samples nor feature axes, so that their order stays the same. So far feature-table heatmap must specify at least one axis to cluster. … --- ## [Allow presence-absence heatmap?](https://forum.qiime2.org/t/allow-presence-absence-heatmap/3022)
**Author:** [@Matilda\_H-D](https://forum.qiime2.org/u/Matilda_H-D)\ **Replies:** 1\ **Last updated:** [February 16, 2018, 11:27pm UTC](https://forum.qiime2.org/t/allow-presence-absence-heatmap/3022 "2018-02-16T23:27:16Z")
Hi there, I was wondering what people would think about adding FeatureTable\[PresenceAbsence\] as an input type to qiime feature-table heatmap? Currently the command only accepts FeatureTable\[Frequency\]. Not a huge deal,… [Next page](https://forum.qiime2.org/tag/heatmap/129.md?match_all_tags=true&page=1&tags%5B%5D=heatmap)