Alpha_div.R Tutorial - sciencesharon/MicrobialSeq GitHub Wiki

Alpha_div.R Tutorial

This is the tutorial for how to use the Alpha_div.R script which has the alpha_div_auto function. This function is for downstream use of either Merged_Abundance_Processing.R or process_abundance_data.py. It takes the input of the read count table along with sample metadata and outputs Alpha Diversity calculations for the Chao1 index, Evenness, Richness, and Shannon Diversity Index. It outputs box plots - either four separate box plots or one stacked box plot - along with statistical comparisons between your given groups using Wilcoxon Rank Sum test and adds the p-value (as stars) for the comparisons to the plots. The alpha diversity calculations are saved as a .csv file and the results of the Wilcoxon Rank Sum test are also each saved as .csv files.

Example Input Files

Read Count Table: readcount_example.csv

Metadata: metadata_example.csv

Function usage

Load the read count data and metadata

read.count <- read.csv("/path/to/readcount_example.csv") metadata <- read.csv("/path/to/metadata_example.csv")

Utilize the alpha_div_auto function:

count_data is the read count table, samples must be in columns and taxa in rows

met is the metadata file - the metadata must have samples in rows which match exactly the samples in the columns of the read count table

comparison_var is the grouping variable (one of the columns in your metadata) by which the data will be compared

stack_plots = TRUE outputs the stacked version of the plot

pdf_height and pdf_width change the dimensions of the output pdf files

output_dir is the destination for the files

alpha_div_auto(count_data = read.count, met = metadata, comparison_var = "Timepoint", stack_plots = FALSE, pdf_height = 5, pdf_width = 5, output_dir = "/path/to/file/destination")

Example Outputs

alpha_data.csv

pwc_chao.csv

pwc_eveness.csv

pwc_richness.csv

pwc_shannon.csv

chao1.pdf

evenness.pdf

richness.pdf

shannon.pdf

combined_plot.pdf