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Sampling model from

Daylight exposure modulates bacterial communities associated with household dust

Fahimipour et al. (2018) doi: 10.1186/s40168-018-0559-4

This repository contains R scripts that recreate sampling models from our manuscript on the experimental effects of light exposures on the dust microbiome.

Instructions

To run:

  1. download this repository and set your working directory
  2. source('./R/util_func.R')

The function sampleSeq() takes parameter values as described in the manuscript. Evaluating sampleSeq(100) will perform 100 model simulations with the same parameter ranges as in the manuscript. An example usage and visualization is:

## Perform 100 simulations with default parameters
res <- sampleSeq(100)

## color palette
col.dude <- magma(15) %>% rev()

##-
## ggplot
##-
ggplot(data = res, aes(x = log10(1 + nw), y = lf)) +
  theme_classic() +
  xlab(expression('log'['10']*' 1 + RSV Abundance')) +
  ylab(expression('Apparent log'['10']*'-fold change following loss of abundant RSVs')) +
  geom_hex(aes(fill = (..count..)/sum(..count..)), bins = 20, alpha = 0.85, size = 0.5, colour = '#f7f7f7') +
  geom_hline(yintercept = 0, linetype = 3, size = 0.75) +
  scale_fill_gradientn(colours = col.dude, trans = 'identity', name = 'Frequency', breaks = pretty_breaks(n = 5)) +
  theme(axis.title = element_text(size = 10))