mia-datasets: miaViz example data

In microbiome/miaViz: Microbiome Analysis Plotting and Visualization

miaViz example data

Description

These example data objects were prepared to serve as examples. See the details for more information.

Usage

data(col_graph)

data(row_graph)

data(row_graph_order)

Format

An object of class tbl_graph (inherits from igraph) of length 26.

An object of class tbl_graph (inherits from igraph) of length 996.

An object of class tbl_graph (inherits from igraph) of length 110.

Details

For *_graph data:

1. “Jaccard” distances were calculated via calculateDistance(genus, FUN = vegan::vegdist, method = "jaccard", exprs_values = "relabundance"), either using transposed assay data or not to calculate distances for samples or features. NOTE: the function mia::calculateDistance is now deprecated.

2. “Jaccard” dissimilarites were converted to similarities and values above a threshold were used to construct a graph via graph.adjacency(mode = "lower", weighted = TRUE).

3. The igraph object was converted to tbl_graph via as_tbl_graph from the tidygraph package.

microbiome/miaViz documentation built on Nov. 23, 2024, 8:59 p.m.