R/mean_occ_diff_plot.R

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

# library(dplyr)
# library(ggpubr)
# library(plotly)
# library(gridExtra)
# source("functions/cores.R")

# There must be Sample_ID and SampleType in map file.

##' @title 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.
##' @param otu a community count data matrix with samples in rows and OTUs/taxa in column,
##' @param sample a sample information data.frame. The rownames must match the sample names in the otu,
##' @param mini_abun the minimum abundance of the loop,
##' @param max_abun the maximum abundance of the loop,
##' @param abun_step the abundance step of the loop,
##' @param mini_thre the minimum threshold of the loop,
##' @param max_thre the maximum threshold of the loop,
##' @param thre_step the threshold step of the loop,
##' @param sample_name the name of a column that containing the sample name,
##' @param sample_group the name of a column that containing the sample type/group,
##' @param ...
##' @details Plots a heatmap showing the mean occurrence frequency difference between core and non-core otu under different minimal abundance and threshold.
##' @return 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)
##' @export

mean_occ_diff_plot <- function(otu, sample, min_abun, max_abun, abun_step, min_thre, max_thre, thre_step, sample_name, sample_group){ # , height, weight

  options(warn=-1)

  #otu = read.csv(otu, sep = ",", header = T, row.names = 1)
  #sample = read.csv(sample, sep = ",", header = T, row.names = 1)
  otu <- data.frame(otu)
  sample <- data.frame(sample)
  p <- dis_occ_loop(otu, sample, min_abun = min_abun, max_abun = max_abun, abun_step = abun_step, min_thre = min_thre, max_thre = max_thre, thre_step = thre_step, sample_name, sample_group)
  p
}