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Some of the things in options should be renamed and moved to a new "view" tab
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This should be fixed by changing the `keep_empty_rows` argument in `parse_classic_otu_table`, note that this option only became available in QIIME 1.6.0-dev ( https://github.com/qiime/qiime/commit/b02…
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i.e. with a white background I can't make the taxa label appear in black
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Note this is a duplicate of [my question on Cross Validated](http://stats.stackexchange.com/questions/71107/how-to-use-r-function-prc-in-package-vegan-to-produce-the-tables-in-van-den)
This is also n…
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Hi Joey,
suggestion for consideration rather than bug.
Sometimes if I label OTUs on a plot using Genus there are labels missing due to that particular taxonomic level being absent for that OTU. In…
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I get double circles whenever I use plot_ordination() and set shape values manually. This is only apparent when I use open symbols and increase the size of the points with geom_point(size)
``` S
wUF1…
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It seems sometimes the otu table files headers have to be commented out; other times they have to be uncommented. For example, the table files created from make_otu_table.py and input to PCoA plotting…
RNAer updated
11 years ago
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The results change based on how many OTUs you want to display.
I caught this error while creating a plot and seeing that the script will send "Warning: invalid value encountered in divide" when doin…
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This script isn't widely used, and would likely be more generally useful if it started with an OTU table, tree, mapping file, and optional list of categories of interest and wrapped the most common do…
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`plot_ordination_biplot()`, formerly `plot_ordination_phyloseq()`, represented a nice first attempt at an easy-to-understand wrapper for making `ggplot2` graphics of ordinations. It was quite biased t…