mean_occ_diff_plot: mean_occ_diff_plot

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

mean_occ_diff_plot

Description

Plots a heatmap showing the mean occurrence frequency difference between core and non-core otu under different minimal abundance and threshold.

Usage

mean_occ_diff_plot(
  otu,
  sample,
  min_abun,
  max_abun,
  abun_step,
  min_thre,
  max_thre,
  thre_step,
  sample_name,
  sample_group
)

Arguments

otu	a community count data matrix with samples in rows and OTUs/taxa in column,
sample	a sample information data.frame. The rownames must match the sample names in the otu,
max_abun	the maximum abundance of the loop,
abun_step	the abundance step of the loop,
max_thre	the maximum threshold of the loop,
thre_step	the threshold step of the loop,
sample_name	the name of a column that containing the sample name,
sample_group	the name of a column that containing the sample type/group,
mini_abun	the minimum abundance of the loop,
mini_thre	the minimum threshold of the loop,

Details

Plots a heatmap showing the mean occurrence frequency difference between core and non-core otu under different minimal abundance and threshold.

Value

A heatmap showing the mean occurrence frequency difference between core and non-core otu under different minimal abundance and threshold.

Examples

 mean_occ_diff_plot(otu, sample, min_abun = 0, max_abun = 400, abun_step = 100, min_thre = 0, max_thre = 0.1, thre_step = 0.02, sample_name, sample_group)

lindan1128/coreMicrobiome documentation built on May 5, 2022, 8:24 p.m.