# Building heatmap using Qiime2r
**URL:** https://forum.qiime2.org/t/building-heatmap-using-qiime2r/25034
**Category:** Other Bioinformatics Tools
**Tags:** qiime2r, heatmap
**Created:** [December 15, 2022, 10:11pm UTC](https://forum.qiime2.org/t/building-heatmap-using-qiime2r/25034 "2022-12-15T22:11:40Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@gcook207](https://forum.qiime2.org/u/gcook207)
#### Post date: [December 15, 2022, 10:11pm UTC](https://forum.qiime2.org/t/building-heatmap-using-qiime2r/25034/1 "2022-12-15T22:11:40Z")
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 I am using:
library(tidyverse)
library(qiime2R)
OTUs\<-apply(OTUs.j, 2, function(x) x/sum(x)\*100)
head(OTUs)
OTUs\<-
data.frame(MeanAbundance=rowMeans(OTUs)) %\>%
rownames\_to\_column("Feature.ID") %\>%
arrange(desc(MeanAbundance)) %\>%
top\_n(30, MeanAbundance) %\>%
pull(Feature.ID)
OTUs %\>%
as.data.frame() %\>%
rownames\_to\_column("Feature.ID") %\>%
gather(-Feature.ID, key="SampleID", value="Abundance") %\>%
mutate(Feature.ID=if\_else(Feature.ID %in% OTUs, Feature.ID, "Remainder")) %\>%
group\_by("SampleID", Feature.ID) %\>%
summarize(Abundance=sum(Abundance)) %\>%
left\_join(metadata) %\>%
mutate(NormAbundance=log10(Abundance+0.01)) %\>%
left\_join(Taxonomy.j) %\>%
mutate(Feature=paste(Feature.ID, Taxon)) %\>%
mutate(Feature=gsub("[kpcofgs]\_\_", "", Feature)) %\>%
mutate('Period'=factor('Period',levels = c("A","B","C")))
ggplot(aes(x=`Period`, y=Feature, fill=NormAbundance)) +
geom\_tile() +
facet\_grid(~`Donor`, scales="free\_x") +
theme\_q2r() +
theme(axis.text.x=element\_text(angle=45, hjust=1)) +
scale\_fill\_viridis\_c(name="log10(% Abundance)")
ggsave("qiime2/image/heatmap.pdf", height=4, width=11, device="pdf")
here is the error I am stuck on:
Error in `summarize()`:
! Problem while computing `Abundance = sum(Abundance)`.
ℹ The error occurred in group 1: "SampleID" =
"SampleID", Feature.ID = "Remainder".
Caused by error in `sum()`:
! invalid 'type' (character) of argument
Run `rlang::last_error()` to see where the error occurred.
The OTUs 'type' is listed as a character in R. Does this need to be changed to a data frame ?
Thank you for your time in advance!
---
### Author:  [@gcook207](https://forum.qiime2.org/u/gcook207)
#### Post date: [December 17, 2022, 6:53am UTC](https://forum.qiime2.org/t/building-heatmap-using-qiime2r/25034/2 "2022-12-17T06:53:26Z")
I am new to R and qiime2r plugin. If I have identified the problem correctly, could you help me in figuring out what function in R I need to use and how to identify the correct location in the code to insert the new function?
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [December 24, 2022, 3:17am UTC](https://forum.qiime2.org/t/building-heatmap-using-qiime2r/25034/3 "2022-12-24T03:17:49Z")
Hello Greta,
Can you run this code and look at the `$Abundance` column?
```R
OTUs %>%
as.data.frame() %>%
rownames_to_column("Feature.ID") %>%
gather(-Feature.ID, key="SampleID", value="Abundance") %>%
mutate(Feature.ID=if_else(Feature.ID %in% OTUs, Feature.ID, "Remainder")) %>%
group_by("SampleID", Feature.ID) %>%
head()
```
That error is telling us something is a character (a.k.a. string or text) instead of a number, and I'm wondering if the abundance column is the problem.
If it is, we can reformat it as numeric before passing it into the summarize() function.
---
### Author:  [@gcook207](https://forum.qiime2.org/u/gcook207)
#### Post date: [January 13, 2023, 3:14pm UTC](https://forum.qiime2.org/t/building-heatmap-using-qiime2r/25034/4 "2023-01-13T15:14:15Z")
Hello Colin,
Thank you for your reply. I ran your code and yes, the abundance column is listed as character.
---
### Author:  [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [January 24, 2023, 4:47pm UTC](https://forum.qiime2.org/t/building-heatmap-using-qiime2r/25034/5 "2023-01-24T16:47:48Z")
Sorry to keep you waiting! In case you have not found this yet, you can convert that column from letters to numbers like this:
```auto
dataframe <- dataframe %>%
mutate(Abundance = as.numeric(Abundance))
```