micro_rocky_mtn: Create Rocky Mountain plots from negative binomial taxa...

In tidyMicro: A Pipeline for Microbiome Analysis and Visualization

Description

Display the magnitude of log p-values for each of the taxa in nb_mods as vertical bars next to each other along the x-axis. The direction of the bars will be determined by the direction of the estimated relationship. The taxa will be color coded by the phylum they belong to, and taxa that have FRD adjusted p-values below your desired significance cutoff for the specified covariate will be labeled

Usage

micro_rocky_mtn(
  modsum,
  ...,
  main = NULL,
  ylab = NULL,
  subtitle = NULL,
  pval_lines = TRUE,
  pval_text = TRUE,
  sig_text = TRUE,
  facet_labels = NULL,
  alpha = 0.05,
  lwd = 2,
  lty = 1
)

Arguments

modsum	The output from nb_mods
...	The covariate you'd like to plot. Must be in the models created by nb_mods
main	Plot title
ylab	y-axis labels
subtitle	Plot subtitle
pval_lines	Logical; include horizonal dashed lines at corresponding p-values
pval_text	Logical; label the y-axis with corresponding p-values
sig_text	Logical; label the taxa with p-values below specified alpha
facet_labels	Labels for different facets if covariate has more than 1 beta coefficient
alpha	Significance cutoff
lwd	Line width for pval_lines
lty	Line type for pval_lines

Value

A ggplot you can add geoms to if you'd like

Author(s)

Charlie Carpenter, Rachel Johnson, Dan Frank

Examples

data(bpd_phy); data(bpd_cla); data(bpd_ord); data(bpd_fam); data(bpd_clin)
otu_tabs = list(Phylum = bpd_phy, Class = bpd_cla,
Order = bpd_ord, Family = bpd_fam)

set <- tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>%
filter(day == 7) ## Only including the first week

## Creating negative binomial models on filtered tidy_micro set
nb_fam <- set %>%
otu_filter(ra_cutoff = 0.1, exclude_taxa = c("Unclassified", "Bacteria")) %>%
nb_mods(table = "Family", bpd1)

nb_fam %>% micro_rocky_mtn(bpd1)

tidyMicro documentation built on Jan. 13, 2021, 6:18 a.m.