Hi community!!!
I want to visualise my data output analysed by mothur pipeline with Phyloseq package. I have gone through the phyloseq tutorial but still confused as I have no idea with R (Although I've successfully installed the necessary packages).
I don't know which outputs from Mothur should I use as input for phyloseq and how to process them before running with phyloseq.
Can anyone please help me. I am really struggling with this.
Hi andres.firrincieli, can I draw your attention for an isuue I am facing?
I am following the tutorial you have provided. I am here at the "a stacked barplot for the class level" of the tutorial. I accordingly used the codes as in tutorial:
# melt to long format (for ggploting)
# prune out phyla below 1% in each sample
# selecting the taxa at the level: Phylum
mdata_class <- mouse_data %>%
tax_glom(taxrank = "Class") %>% # agglomerate at phylum level
transform_sample_counts(function(x) {x/sum(x)} ) %>% # Transform to rel. abundance
psmelt() %>% # Melt to long format
filter(Abundance > 0.01) %>% # Filter out low abundance taxa
arrange(Class) # Sort data frame alphabetically by phylum
str(mdata_class)
Here clearly number of different kingdom, phylums, classes is shown which is 1, 9, 15 respectively. But in my dataset I am using the same code, but the output doesn't show number of different classes. As a result I am unable to use colours for them:
Hi DC,
here is a tutorial on how to build a
phyloseq
object from mothur files.Hope this helps!
Thanks andres!!! Can you please help me with this error? I have imported mothur files with these codes:
But, after
head(phyloseq)
, I am getting the following ERROR:Thanks and Regards, DC7
you can't use
head()
on a S4 object. To inspect the OTU table simply useotu_table(physeq)
. For the taxonomytax_table(physeq)
.Source