joey711/phyloseq-demo

Extended demonstrations of the phyloseq package

phyloseq-demo's Issues

outsource demo sections where appropriate

Some demo sections have more-updated tutorials on the phyloseq main page tutorials. These sections should simply link to those and show nothing, with the exception of material that is new, but too long, involved, specific, or otherwise not appropriate to migrate to the main page tutorials. This will save time rebuilding demo pages, keep the connection between these two documentation sites robust, and make the management and maintenance of demo code (both demo and main page), much easier according to the DRY principle.

Add filter_taxa() to preprocessing section of demo

See the documentation of filter_taxa() for some ideas, as well as genefilter::genefilter.

use of 'unsafe scripts'

The Phyloseq-demo page shows this warning in Chrome.

This happens because it tries to load this .css file without using https.
http://joey711.github.io/phyloseq/markdown.css

Also, this file no longer exists, so removing this line would be an easy fix.

If this is not a priority compared to the new site, feel free to close this issue.

restroom biogeography demo

Dear Paul and Susan

First of all, many thanks for all the effort you put into this package, it is much appreciated. It has certainly made my analysis time easier though I am still new to R.

I have been following the Restroom Biogeography example that perhaps you wrote up (I didn't see any names), and I'm having some challenges. I will try create a Pull request to fix the link in the tutorial.

Ok, so under Figure 1, Panel B – Gender and Figure 1 Part A (remake), attempt 2 there is a repair function you use. I was hoping you could expand a little on it? I try to run this, obviously replacing the variable names with the ones I am using, but instead of having them fixed, the variable is removed from the phyloseq object. Obviously they need fixing because if I look at the variables before attempting to fix them it is just a list of NAs. I still find R syntax nightmarish, so I would be most grateful for pointers for what I could change.

Thirdly, under Figure 2 - Dimensional Reduction and Figure 2 - Reproduced I am having trouble plotting the PCoA. I keep getting "Error: A continuous variable can not be mapped to shape". StackOverflow suggests converting the variable using as.factor, but I maybe mistakenly think that phyloseq would have taken care of this.

I'm using Phyloseq 1.14.0, ggplot 2.1.0 and rdputils 1.2

Kind regards
Liam

plot_bar

Dear users,
My name is Husen Zhang. I use QIIME followed by phyloseq on microbiome data. exact command follows, but the problem is that the order of "Firmicutes" and "Bacteroidetes" are inconsistent across the samples. For example, some has "Firmicutes" on top, some has "Bacteroidetes" on top:

the exact command run was:
plot_bar(phylum, fill = 'Phylum', x = 'mouse_id') + geom_bar(stat = 'identity', position = 'stack') + scale_fill_brewer(palette = "Set1", guide=guide_legend(rev=TRUE)) + ylab("Percent")