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Plot Bray-Curtis increase over ranked OTU/ASVs

Source: R/plot_identified_core.R
plot_identified_core.Rd

Visualize the cumulative normalized mean Bray-Curtis increase returned by identify_core(), over ranked OTU/ASVs and shows cutoff points for elbow percent increase methods.

Usage

plot_identified_core(
  bray_curtis_ranked,
  elbow,
  lastCall,
  increase_value = 0.02,
  dataset_name = NULL
)

Arguments

bray_curtis_ranked

A tibble as returned by identify_core()$bray_curtis_ranked.

elbow

The number of OTU/ASVs identified by the elbow method (Integer).

lastCall

The number of OTU/ASVs identified by the last percent Bray-Curtis increase method (Integer).

increase_value

The percent increase value in decimal (e.g. 0.02) used for the Bray-Curtis increase method.

dataset_name

Optional character string. When provided, it is prepended to the plot title (e.g. "Switchgrass"). Default NULL (no prefix).

Value

A list containing: 1) df_for_plot, a data frame used for plotting, and 2) plot_identified_core, a ggplot object visualizing the Bray-Curtis increase with annotated cutoff points.

Details

The function converts rank to integers and zooms the x-axis to the first 1.2 * lastCall ranks. Label positions are computed dynamically from the observed proportionBC range to avoid overlap.

See also

identify_core()

identify_core

Examples

library(BRCore)
data("switchgrass_core", package = "BRCore")

p <- plot_identified_core(
  bray_curtis_ranked = switchgrass_core$bray_curtis_ranked,
  elbow = switchgrass_core$elbow,
  lastCall = switchgrass_core$bc_increase,
  increase_value = switchgrass_core$increase_value
)
print(p)
#> $df_for_plot
#> # A tibble: 40 × 13
#>    rank  rank_num otu_added  MeanBC proportionBC IncreaseBC elbow_slope_diffs
#>    <fct>    <int> <chr>       <dbl>        <dbl>      <dbl>             <dbl>
#>  1 1            1 OTU47     0.00638       0.0124      NA            -0.000719
#>  2 2            2 OTU2      0.0469        0.0913       7.35          0.0196  
#>  3 3            3 OTU6      0.0962        0.187        2.05          0.0294  
#>  4 4            4 OTU21     0.104         0.203        1.08          0.0239  
#>  5 5            5 OTU10     0.109         0.212        1.04          0.0199  
#>  6 6            6 OTU7      0.136         0.266        1.25          0.0211  
#>  7 7            7 OTU4      0.210         0.410        1.54          0.0287  
#>  8 8            8 OTU430    0.219         0.427        1.04          0.0262  
#>  9 9            9 OTU23     0.227         0.441        1.03          0.0241  
#> 10 10          10 OTU18     0.237         0.462        1.05          0.0227  
#> # ℹ 30 more rows
#> # ℹ 6 more variables: delta_pct_max_BC <dbl>, is_BC_core <lgl>,
#> #   last_pctBC_cutoff <lgl>, is_elbow_core <lgl>, last_elbow_cutoff <lgl>,
#> #   rank_fac <fct>
#> 
#> $plot_identified_core

#>