core_heatmap: Core Heatmap
In microbiome: Microbiome Analytics
Description
Usage
Arguments
Value
Author(s)
References
Description
Core heatmap.
Usage
1
core_heatmap(x, dets, cols, min.prev, taxa.order)
Arguments
x
OTU matrix
dets
A vector or a scalar indicating the number of intervals
in (0, log10(max(data))). The dets are calculated for relative
abundancies.
cols
colours for the heatmap
min.prev
If minimum prevalence is set, then filter out those
rows (taxa) and columns (dets) that never exceed this prevalence.
This helps to zoom in on the actual core region of the heatmap.
taxa.order
Ordering of the taxa.
Value
Used for its side effects
Author(s)
Contact: Leo Lahti microbiome-admin@googlegroups.com
References
A Salonen et al. The adult intestinal core microbiota is determined by
analysis depth and health status. Clinical Microbiology and Infection
18(S4):16 20, 2012.
To cite the microbiome R package, see citation('microbiome')
microbiome documentation built on Nov. 8, 2020, 5:08 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) References
Description
Core heatmap.
Usage
1 | core_heatmap(x, dets, cols, min.prev, taxa.order)
|
Arguments
x |
OTU matrix |
dets |
A vector or a scalar indicating the number of intervals in (0, log10(max(data))). The dets are calculated for relative abundancies. |
cols |
colours for the heatmap |
min.prev |
If minimum prevalence is set, then filter out those rows (taxa) and columns (dets) that never exceed this prevalence. This helps to zoom in on the actual core region of the heatmap. |
taxa.order |
Ordering of the taxa. |
Value
Used for its side effects
Author(s)
Contact: Leo Lahti microbiome-admin@googlegroups.com
References
A Salonen et al. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16 20, 2012. To cite the microbiome R package, see citation('microbiome')
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.