NMDS





Select a file  Example

Select a file  Example


Select a file   Example









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Function:
Non-metric multidimensional scaling (NMDS) is a rank-based and indirect gradient analysis approach which produces an ordination based on a distance or dissimilarity matrix.


Input:

(1) The input file can be abundance table(OTU,species,funtion abundance table)or similarity distance matrix

(2)Grouping file is optional. The tool supports no more than 2 grouping information in a single sample.

(3) The input file should be a tab-delimited “.txt” file


Parameters:

(1)Dot size:Dot size: define the dots size(the default value is 3)

(2)Group name:define the group name

(3)Dot transparency:define the dots transparency if case of overlapping of dots

Output:

nmds_sites.xls:document dot sites in an NMDS plot.


nmds_plot.pdf/png: NMDS_plot.png/pdf: NMDS plot of NMDS1-NMDS2, NMDS1-NMDS3 and NMDS2-NMDS3.


Tool machinery:

(1)If importing an OTU table, the tool will first normalize each OTU in the relative abundance, then calculate sample similarity distance of Bray-Curtis by R. Finally, PCoA is performed in R and plotted using ggplot2 software.

(2)If importing similarity distance matrix (e.g. Unifrac distance), the PCoA tool will calculate and plot a chart directly from the input matrix.

例子文件:

Abundance table    Grouping file1    Grouping file2

Output:


生物云平台 生物云平台 生物云平台