taxa_boxplot: Function to make boxplots of taxa counts or relative...

Description Usage Arguments Value Examples

View source: R/box_plot.R

Description

A function to make boxplots of one specified taxa relative abundance with the option to stratify by a factor variable

Usage

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taxa_boxplot(
  micro_set,
  taxa,
  ...,
  y = ra,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  subtitle = NULL,
  legend_title = NULL
)

Arguments

micro_set

A tidy_micro data set

taxa

A character string. The name of the taxa of interest

...

The factor variable you'd like to stratify by

y

The taxa information

xlab

x-axis label

ylab

y-axis label

main

Plot title

subtitle

Subtitle for the plot

legend_title

Title of plot legend

Value

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

Examples

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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

set %>%
taxa_boxplot("Firmicutes/Bacilli/Bacillales/Staphylococcaceae", bpd1)

Example output

Loading required package: tidyverse
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.3.2purrr   0.3.4tibble  3.0.4dplyr   1.0.2tidyr   1.1.2stringr 1.4.0readr   1.4.0forcats 0.5.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()dplyr::lag()    masks stats::lag()
Contains 74 libraries from OTU files.

Summary of sequencing depth:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   8851   24938   33314   36650   43590   97408 

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