qiime2R unable to load package.

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1

I am trying to use the qiime2R package to make the pcoa plot. Had been able to install library(tidyverse) devtools::install_github(“jbisanz/qiime2R”). despite all these, I can't still load qiime2R. please I need some quick help @jbisanz @yanxianl

2

It sounds like qiime2R did not successfully install. Check the messages after running devtools::install_github(“jbisanz/qiime2R”) and there should be an informative message in there.

3

oh yes you are right. it been fixed thank you.

4

i got some other errors of concern here please. first is when trying to make the heatmap
at first instance i got this error

SVs <-read_qza("D:/Qiime222/BacAr_filter_table.qza")
taxonomy<-read_qza("D:/Qiime222/gg_taxonomy.qza")
SVs<-apply(SVs, 2, function(x) x/sum*100)
Error in apply(SVs, 2, function(x) x/sum * 100) :
dim(X) must have a positive length.

Also here

SVsToPlot<-

  • data.frame(MeanAbundance=rowMeans(SVs)) %>%
  • rownames_to_column("Feature.ID") %>%
  • arrange(desc(MeanAbundance)) %>%
  • top_n(30, MeanAbundance) %>%
  • pull(Feature.ID)
    Error in rowMeans(SVs) : 'x' must be an array of at least two dimensions

While trying to make plot PCOA i came across this.

uwunifrac$data$Vectors %>%

  • + select(SampleID, PC1, PC2) %>%

  • + left_join(metadata55) %>%

  • + left_join(shannon) %>%

  • + ggplot(aes(x=PC1, y=PC2, color=`Period`, shape=`Treatment`, size=shannon)) + geom_point(alpha=0.5) + theme_q2r() + scale_shape_manual(values=c(16,1), name="Treatment") + scale_size_continuous(name="Shannon Diversity") + scale_color_discrete(name="Period") + stat_ellipse()

Error in select(SampleID, PC1, PC2) : object 'SampleID' not found

Please i will be glad with some help out here. Thank you in advance

5

If you want the data from the artifact, you need to add $data to the end,

6

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