qiime2R: changing facets

Community Plugin Support
1

Hi, thank you for your very useful package.

I am in the middle of making my heatmap, I change several script to suit my data.
Now I am wondering the possibility of changing the order of the facet. Could you change the order of the body_site of the facet?
For example, in your attached figure, they were ordered like gut;left palm;right palm;tongue. What should be added to the script/command to change it in custom order? E.g right palm;left palm; tongue;gut ??

I try the factor() function with levels the “body_site” but error that dollar sign are not accepted in atomic vector appeared.

Thank you.

2

You have the right idea, the line you would want is:

mutate(`body-site`=factor(`body-site`, levels=c("right palm","left palm","gut","tongue")))

Perhaps it was an issue relating to the “-”?

Full code below:


library(tidyverse)
library(qiime2R)

metadata<-read_q2metadata("~/GitHub/qiime2R/inst/artifacts/2020.2_moving-pictures/sample-metadata.tsv")
SVs<-read_qza("~/GitHub/qiime2R/inst/artifacts/2020.2_moving-pictures/table.qza")$data
taxonomy<-read_qza("~/GitHub/qiime2R/inst/artifacts/2020.2_moving-pictures/taxonomy.qza")$data

SVs<-apply(SVs, 2, function(x) x/sum(x)*100) #convert to percent

SVsToPlot<-  
  data.frame(MeanAbundance=rowMeans(SVs)) %>% #find the average abundance of a SV
  rownames_to_column("Feature.ID") %>%
  arrange(desc(MeanAbundance)) %>%
  top_n(30, MeanAbundance) %>%
  pull(Feature.ID) #extract only the names from the table

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")) %>% #flag features to be collapsed
  group_by(SampleID, Feature.ID) %>%
  summarize(Abundance=sum(Abundance)) %>%
  left_join(metadata) %>%
  mutate(NormAbundance=log10(Abundance+0.01)) %>% # do a log10 transformation after adding a 0.01% pseudocount. Could also add 1 read before transformation to percent
  left_join(taxonomy) %>%
  mutate(Feature=paste(Feature.ID, Taxon)) %>%
  mutate(Feature=gsub("[kpcofgs]__", "", Feature)) %>% # trim out leading text from taxonomy string
  mutate(`body-site`=factor(`body-site`, levels=c("right palm","left palm","gut","tongue"))) %>%
  ggplot(aes(x=SampleID, y=Feature, fill=NormAbundance)) +
  geom_tile() +
  facet_grid(~`body-site`, 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") # save a PDF 3 inches by 4 inches
1 Like
3

Thank you! It works!
I initially try it like this

mutate(SVs$body-site=factor(SVs$body-site, levels=c("right palm","left palm","gut","tongue")))
something like that, and I dont know about where to put the code. Thanks

4

That would have worked perfectly if you were not using the pipe/mutate function!