Building heatmap using Qiime2r

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1

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).
:information_source: 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!

2

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?

3

Hello Greta,

Can you run this code and look at the $Abundance column?

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.

4

Hello Colin,

Thank you for your reply. I ran your code and yes, the abundance column is listed as character.

5

Sorry to keep you waiting! In case you have not found this yet, you can convert that column from letters to numbers like this:

dataframe <- dataframe %>%
  mutate(Abundance = as.numeric(Abundance))
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