phyloseq | analyze phylogenetic sequencing data ; and to reproducibly | Genomics library

I tried to extract the nrow inside of a loop but it keep the same number of the last count for all interactions of the loop, the problem correspond to the lines

I need to convert my OTU table from my phyloseq object into a data frame so that I can use it to run PICRUSt2, but as.data.frame(physeq@otu_table) won't make it a data frame. I tried pie<-as.matrix(physeq@otu_table) and when I say is.matrix(pie) #it says TRUE, but when I say class(pie) #it says [1] "otu_table" attr(,"package") [1] "phyloseq" It wont even pretend to be a data frame:

I am trying to change text label sizes inside my plot (not the axes, rather the label annotations)

I am working with a phyloseq object but I don't think that matters. Here is the code and the output. Any suggestions?

I analyse microbiome data using

I am using plot_bar function in R to illustrate some data from a phyloseq class. I want to add some different colors to my plot, here the pallette Paired from the RColorBrewer package. For some reasons the bars end up still having the default color around them. Here you can see how it looks like: https://imgur.com/a/VSBvwtk Any way I could get rid of them?

I am trying to write output from permutation analysis by using below code but it shows error, could you please suggest how I can resolve this error?

When install any new package I get errors saying Rtools is not found. I followed the manual install instructions for Rtools but still get the same error message.

I am currently trying to knit an R markdown document to html (or pdf) where in a certain chunk I generate multiple plots. I specify the captions through the fig.cap argument in the chunk options with a vector of the same length as the number of plots. However, for this to work the chunk option message has to be TRUE. The issue starts when a ggplot2 object is generated by a function in the chunk and I want to apply a new fill with viridis::scale_fill_viridis. Which is fine, but inevitably throws a message/warning that there is already a fill applied to the ggplot2 object and that the viridis will replace it (Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale). I do not want to get this into the output of my markdown html. Using suppressMessages apparently also suppresses the html (and pdf!) captions. So my question is: is there a way to "unset" the existing scales attribute to avoid this message being generated? Short from that my only other option would be to dive into the code that generated the object in the first place. Or: is there a way that knitr preserves captions when the chunk option messages=F?

A minimal working example would be the following code in an R markdown document: