func_rank_plot: func_rank_plot

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

func_rank_plot

Description

Plots TPM vs ranked otu and avg occ vs avg TPM.

Usage

func_rank_plot(functional_profile, sample, mini_tpm, threshold)

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,
mini_tpm	a value indicating whether the function is present,
threshold	a value indicating the final percent increase in beta-diversity,

Details

Plots TPM vs ranked otu and avg occ vs avg TPM.

Value

A scatter plot showing the relationship between TPM and ranked otu with color denoting and core or non-core functional otu and a line indicating the threshold and a scatter plot showing the relationship between average occurancy and average TPM with color denoting and core or non-core functional otu and a line indicating the threshold.

Examples

 func_rank_plot(functional_profile, sample, mini_tpm=10000, threshold=0.5)

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