rare_stacked: Visualize the number of observations per sample.

In cmmr/rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

Visualize the number of observations per sample.

Description

Visualize the number of observations per sample.

Usage

rare_stacked(
  biom,
  rline = TRUE,
  counts = TRUE,
  labels = TRUE,
  y.trans = "log10",
  ...
)

Arguments

biom	An rbiom object, such as from as_rbiom(). Any value accepted by as_rbiom() can also be given here.
rline	Where to draw a horizontal line on the plot, intended to show a particular rarefaction depth. Set to TRUE to show an auto-selected rarefaction depth, FALSE to not show a line, or an integer for a custom position. Default: TRUE.
counts	Display the number of samples and reads remaining after rarefying to rline reads per sample. Default: TRUE.
labels	Show sample names under each bar. Default: TRUE.
y.trans	The transformation to apply to the y-axis. Visualizing differences of both high- and low-abundance taxa is best done with a non-linear axis. Options are: "sqrt" - square-root transformation "log1p" - log(y + 1) transformation NULL - no transformation These methods allow visualization of both high- and low-abundance taxa simultaneously, without complaint about 'zero' count observations. Default: "sqrt"
...	Additional parameters to pass along to ggplot2 functions. Prefix a parameter name with r. to ensure it gets passed to (and only to) geom_hline. For instance, r.color = "black" ensures only the horizontal rarefaction line has its color set to "black".
trans	Y-axis transformation. Options are "log10" or NULL. Default: "log10".

Value

A ggplot2 plot.
The computed data points and ggplot command are available as ⁠$data⁠ and ⁠$code⁠, respectively.

See Also

Other rarefaction: rare_corrplot(), rare_multiplot(), rarefy(), rarefy_cols(), sample_sums()

Other visualization: adiv_boxplot(), adiv_corrplot(), bdiv_boxplot(), bdiv_corrplot(), bdiv_heatmap(), bdiv_ord_plot(), plot_heatmap(), rare_corrplot(), rare_multiplot(), stats_boxplot(), stats_corrplot(), taxa_boxplot(), taxa_corrplot(), taxa_heatmap(), taxa_stacked()

Examples

    library(rbiom)
    
    rare_stacked(hmp50)
    
    rare_stacked(hmp50, rline = 500, r.size = 2, r.linetype = "twodash")
    
    fig <- rare_stacked(hmp50, counts = FALSE)
    fig$code
    

cmmr/rbiom documentation built on April 28, 2024, 6:38 a.m.