Galaxy |

Create three-dimensional PCoA plots (version 1.9.1.0)

Filepath of a coordinates file to create a PCoA plot:

Mapping file:

Number of axes to be incorporated in the plot:

Only 3 will be displayed at any given time but this option modifies how many axes you can use for your visualization. Note that Emperor will only use the axes that explain more than 0.5% (this will be shown as 1% in the GUI) of the variability

Add to the output categories of the mapping file the columns where all values are different?:

If the result of one of the concatenated fields in --color_by is a column where all values are unique, the resulting column will get removed as well

Comma-sparated category(ies) used to add connecting lines (vectors) between samples:

The first category specifies the samples that will be connected by the vectors, whilst the second category (optionally) determines the order in which the samples will be connected

Comma-separated list of metadata categories (column headers) to color by in the plots:

The categories must match the name of a column header in the mapping file exactly. Multiple categories can be listed by comma separating them without spaces. The user can also combine columns in the mapping file by separating the categories by && without spaces

Overpass the error raised when the coordinates file contains samples that are not present in the mapping file?:

Be aware that this is very misleading as the PCoA is accounting for all the samples and removing some samples could lead to erroneous/skewed interpretations

Add a summarized taxa file?:

Number of segments to generate any spheres:

This includes the samples, the taxa (biplots), and the confidence intervals (jackknifing). Higher values will result in better quality but can make the plots less responsive, also it will make the resulting SVG images bigger

Allow the percent variation explained by the axis to be below one?:

The default behavior is to multiply by 100 all values if PC1 is < 1.0

Add custom axes?:

What it does

This tool calculates alpha diversity, or within-sample diversity, using an OTU table.

The resulting file(s) is a tab-delimited text file, where the columns correspond to alpha diversity metrics and the rows correspond to samples and their calculated diversity measurements. When a folder is given as input (-i), the script processes every otu table file in the given folder, and creates a corresponding file in the output directory.

More information about this tool is available on QIIME documentation.