dacomp.plot_reference_scores: Plot histogram of median SD statistics from a reference...

In barakbri/dacomp: Non parametric differential abundance testing for microbiome counts data.

Description

Plot histogram of median SD statistics from a reference selection result object

Usage

dacomp.plot_reference_scores(
  ref_select,
  label = "Histogram of medianSD statistic, across taxa",
  quantiles_to_plot = c(0.5, 0.7, 0.9),
  breaks_param = 30
)

Arguments

ref_select	Computation result of dacomp.select_references
label	Histogram label.
quantiles_to_plot	Percentiles marked by vertical lines. Default value is c(0.5,0.7,0.9).
breaks_param	Passed as argument with the same name to the hist function.

Examples

## Not run: 
library(dacomp)

set.seed(1)

data = dacomp.generate_example_dataset.two_sample(m1 = 100,
       n_X = 50,
       n_Y = 50,
       signal_strength_as_change_in_microbial_load = 0.1)

#select references: (may take a minute)
result.selected.references = dacomp.select_references(X = data$counts,
                                                     median_SD_threshold = 0.6, #APPLICATION SPECIFIC
                                                     verbose = T)

length(result.selected.references$selected_references)

#plot the reference selection scores (can also be used to better set the median SD threshold)
dacomp.plot_reference_scores(result.selected.references)


## End(Not run) 

barakbri/dacomp documentation built on June 17, 2021, 11:20 p.m.