mean_func_occ_diff_plot: mean_func_occ_diff_plot

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

mean_func_occ_diff_plot

Description

Plots a heatmap showing the mean occurrence frequency difference between core and non-core functional otu under different minimal tpm and thresholds.

Usage

mean_func_occ_diff_plot(
  functional_profile,
  sample,
  min_tpm,
  max_tpm,
  tpm_step,
  min_thre,
  max_thre,
  thre_step
)

Arguments

functional_profile	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_tpm	the maximum TPM of the loop,
max_thre	the maximum threshold of the loop,
thre_step	the threshold step of the loop,
mini_tpm	the minimum TPM of the loop,
abun_step	the TPM step 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 functional otu under different minimal tpm and thresholds.

Value

A heatmap showing the mean occurrence frequency difference between core and non-core functional otu under different minimal tpm and thresholds.

Examples

 mean_func_occ_diff_plot(functional_profile, sample, min_tpm = 0, max_tpm = 4000, tpm_step = 100, min_thre = 0, max_thre = 0.1, thre_step = 0.02)

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