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Hello! I'm fairly new to your package, apologies if this issue is a syntax thing on my end. I'm trying to create a heatmap of a bacterial community dataset, but have run into an error. Here's my code and the error that I run into:
Top NA OTUs selected
Error in seq_len(n) : argument must be coercible to non-negative integer
For context, I subsetted my phyloseq object to show the top 50 ASVs/OTUs before using this function to deal with a separate error. My thinking was that since some of my OTUs have very low abundances, the log10 transformation was producing negative values. However, I get the same error when I use "compositional" and "NA" for the transformation argument. This phyloseq object is transformed to relative abundances, but I also ran into this error using raw read counts. Any suggestions on how to troubleshoot?
Thanks,
Gillian
The text was updated successfully, but these errors were encountered:
Hello! I'm fairly new to your package, apologies if this issue is a syntax thing on my end. I'm trying to create a heatmap of a bacterial community dataset, but have run into an error. Here's my code and the error that I run into:
bact.heat <- plot_taxa_heatmap(top50.phy, subset.top = NA,
VariableA=c("tissue_type","field"),
heatcolors = grad_ab_pal,
transformation = "log10",
cluster_rows = T,
cluster_cols = T,
show_colnames = F,
annotation_colors=meta_colors)
Top NA OTUs selected
Error in seq_len(n) : argument must be coercible to non-negative integer
For context, I subsetted my phyloseq object to show the top 50 ASVs/OTUs before using this function to deal with a separate error. My thinking was that since some of my OTUs have very low abundances, the log10 transformation was producing negative values. However, I get the same error when I use "compositional" and "NA" for the transformation argument. This phyloseq object is transformed to relative abundances, but I also ran into this error using raw read counts. Any suggestions on how to troubleshoot?
Thanks,
Gillian
The text was updated successfully, but these errors were encountered: