qiime2r dyplr errro

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1

i faced a problem while i was running qiime2r

i applied codes present in this Tutorial in the following link:

[qiime2r toturial]( Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R - Community Contributions / Tutorials - QIIME 2 Forum)

#shannon diversity

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drawing shannon diversity versus time by this code:
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metadata %>%
filter(!is.na(shannon)) %>%
ggplot(aes(x=days-since-experiment-start, y=shannon, color=body-site)) +
stat_summary(geom="errorbar", fun.data=mean_se, width=0) +
stat_summary(geom="line", fun.data=mean_se) +
stat_summary(geom="point", fun.data=mean_se) +
xlab("Days") +
ylab("Shannon Diversity") +
theme_q2r() + # try other themes like theme_bw() or theme_classic()
scale_color_viridis_d(name="Body Site") # use different color scale which is color blind friendly
ggsave("Shannon_by_time.pdf", height=3, width=4, device="pdf") # save a PDF 3 inches by 4 inches

results in this error:

Error: Problem with filter() input ..1.
i Input ..1 is !is.na(shannon).
x Input ..1 must be of size 34 or 1, not size 31.
qiime2r tutorial
sample-metadata.tsv (2.0 KB) qiime2rshannon.qza (69.1 KB) qiime2rtable.qza (52.9 KB) qiime2rtaxonomy.qza (92.4 KB)

2

Interesting, it would appear that for some reason your shannon data has been read in as a table object other than a data.frame. If you ever have this issue in the future you can use use the as.data.frame() function like this:

shannon<-shannon$data %>% as.data.frame() %>% rownames_to_column("SampleID")

I also note in your shannon diversity file, the metric is labelled as shannon_entropy so you will need to keep that in mind when you make you plot.