# Qiime2R Heatmap construction challenges

**URL:** https://forum.qiime2.org/t/qiime2r-heatmap-construction-challenges/24033
**Category:** Other Bioinformatics Tools
**Tags:** qiime2r, heatmap
**Created:** [August 30, 2022, 8:33pm UTC](https://forum.qiime2.org/t/qiime2r-heatmap-construction-challenges/24033 "2022-08-30T20:33:03Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![tafara\_bute](https://forum.qiime2.org/user_avatar/forum.qiime2.org/tafara_bute/32/14065_2.png) [@tafara\_bute](https://forum.qiime2.org/u/tafara_bute)
#### Post date: [August 30, 2022, 8:33pm UTC](https://forum.qiime2.org/t/qiime2r-heatmap-construction-challenges/24033/1 "2022-08-30T20:33:03Z")

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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

 ![heatmap](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/1/10125563734da93492eea293b156069d82363d28.png).  
Please help to guide me through, where I could have missed it. Below is the code I used to run the analysis.

library(tidyverse)  
library(qiime2R)

metadata\<-read\_q2metadata("sample-metadata.txt")  
SVs\<-read\_qza("table.qza")$data  
taxonomy\<-read\_qza("taxa.qza")$data

SVs\<-apply(SVs, 2, function(x) x/sum(x)\*100)

SVsToPlot\<-  
data.frame(MeanAbundance=rowMeans(SVs)) %\>%  
rownames\_to\_column("Feature.ID") %\>%  
arrange(desc(MeanAbundance)) %\>%  
top\_n(30, MeanAbundance) %\>%  
pull(Feature.ID)

SVs %\>%  
as.data.frame() %\>%  
rownames\_to\_column("Feature.ID") %\>%  
gather(-Feature.ID, key="SampleID", value="Abundance") %\>%  
mutate(Feature.ID=if\_else(Feature.ID %in% SVsToPlot, Feature.ID, "Remainder")) %\>%  
group\_by(SampleID, Feature.ID) %\>%  
summarize(Abundance=sum(Abundance)) %\>%  
left\_join(metadata) %\>%  
mutate(NormAbundance=log10(Abundance+0.01)) %\>%  
left\_join(taxonomy) %\>%  
mutate(Feature=paste(Feature.ID, Taxon)) %\>%  
mutate(Feature=gsub("[kpcofgs]\_\_", "", Feature)) %\>%  
ggplot(aes(x=SampleID, y=Feature, fill=NormAbundance)) +  
geom\_tile() +  
facet\_grid(~`depth`, scales="free\_x") +  
theme\_q2r() +  
theme(axis.text.x=element\_text(angle=45, hjust=1)) +  
scale\_fill\_viridis\_c(name="log10(% Abundance)")  
ggsave("heatmap.pdf", height=4, width=11, device="pdf")

Thank you in advance

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [October 1, 2022, 2:33am UTC](https://forum.qiime2.org/t/qiime2r-heatmap-construction-challenges/24033/2 "2022-10-01T02:33:32Z")

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