ggplot2 version of ALDEx2 diagnostic plots

Creates ggplot2 versions of the four ALDEx2 diagnostic plot types: MW (Bland-Altman style), MA, volcano, and volcano.var. Supports faceting by a name column, making it suitable for output from aldex_lpq().

Usage

gg_aldex_plot(
  x,
  type = c("MW", "MA", "volcano", "volcano.var"),
  test = c("welch", "wilcox", "effect", "both"),
  cutoff.pval = 0.05,
  cutoff.effect = 1,
  rare = 0,
  all.col = "grey30",
  called.col = "red",
  rare.col = "black",
  point.size = 1.5,
  point.alpha = 0.4
)

Arguments

x: (data.frame or tibble, required) ALDEx2 results, typically from ALDEx2::aldex() or aldex_lpq(). Must contain columns diff.btw, diff.win, rab.all, and effect. When test is "welch", column we.eBH is required; when "wilcox", column wi.eBH is required.
type: (character, default "MW") Plot type. One of "MW" (dispersion vs difference), "MA" (abundance vs difference), "volcano" (difference vs -log10 q-value), or "volcano.var" (dispersion vs -log10 q-value).
test: (character, default "welch") Statistical test used for significance calling. One of "welch", "wilcox", "effect", or "both" (effect + welch).
cutoff.pval: (numeric, default 0.05) q-value threshold for significance.
cutoff.effect: (numeric, default 1) Effect size threshold (must be >= 0.5 when test is "effect" or "both").
rare: (numeric, default 0) Abundance threshold below which taxa are marked as rare (only used for MW and MA plots).
all.col: (character, default "grey30") Color for non-significant points.
called.col: (character, default "red") Color for significant points.
rare.col: (character, default "black") Color for rare taxa points.
point.size: (numeric, default 1.5) Size of points.
point.alpha: (numeric, default 0.4) Alpha transparency of non-significant points.

Value

A ggplot2 object. If x contains a name column (e.g., from aldex_lpq()), the plot is faceted by name.

Details

This function reimplements ALDEx2::aldex.plot() using ggplot2, providing a more customizable and composable output. The four plot types correspond to the original ALDEx2 types:

MW: Bland-Altman style: within-condition dispersion (x) vs between-condition difference (y), with +/-1 effect size lines.
MA: MA plot: median log2 relative abundance (x) vs median log2 difference (y).
volcano: Volcano plot: median log2 difference (x) vs -log10 q-value (y).
volcano.var: Variance volcano: median log2 dispersion (x) vs -log10 q-value (y).

Examples


data_fungi_high <- multiply_counts_pq(data_fungi, "Height", "High",
  4,
  prop_taxa = 0.1, seed = 42
)
#> Modified 142 taxa in 41 matched samples

aldex_pq(data_fungi_high,
  bifactor = "Height",
  modalities = c("Low", "High")
) |>
  gg_aldex_plot()
#> Taxa are now in rows.
#> aldex.clr: generating Monte-Carlo instances and clr values
#> conditions vector supplied
#> operating in serial mode
#> aldex.scaleSim: adjusting samples to reflect scale uncertainty.
#> aldex.ttest: doing t-test
#> aldex.effect: calculating effect sizes


lpq <- list_phyloseq(
  list(
    fungi = data_fungi,
    fungi_height = data_fungi_high
  ),
  same_bioinfo_pipeline = FALSE
)
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: ROBUSTNESS
#> ℹ 185 common samples, 1420 common taxa
#> ✔ list_phyloseq created (ROBUSTNESS)
# From aldex_lpq (faceted by name)
lpq_res <- aldex_lpq(lpq,
  bifactor = "Height",
  modalities = c("Low", "High")
)
#> Running ALDEx2 on 2 phyloseq objects
#> Bifactor: Height
#> → Processing: fungi
#> Taxa are now in rows.
#> aldex.clr: generating Monte-Carlo instances and clr values
#> conditions vector supplied
#> operating in serial mode
#> aldex.scaleSim: adjusting samples to reflect scale uncertainty.
#> aldex.ttest: doing t-test
#> aldex.effect: calculating effect sizes
#> → Processing: fungi_height
#> Taxa are now in rows.
#> aldex.clr: generating Monte-Carlo instances and clr values
#> conditions vector supplied
#> operating in serial mode
#> aldex.scaleSim: adjusting samples to reflect scale uncertainty.
#> aldex.ttest: doing t-test
#> aldex.effect: calculating effect sizes
gg_aldex_plot(lpq_res, type = "MA")

gg_aldex_plot(lpq_res, type = "MW", test = "wilcox")


gg_aldex_plot(lpq_res, type = "volcano")

gg_aldex_plot(lpq_res, type = "volcano.var")



gingival_pq <-
  MicrobiomeBenchmarkData::getBenchmarkData("HMP_2012_16S_gingival_V35_subset",
    dryrun = FALSE
  )[[1]] |>
  mia::convertToPhyloseq()
#> Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
#> Also defined by ‘Rmpfr’
#> Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
#> Also defined by ‘Rmpfr’
#> Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
#> Also defined by ‘Rmpfr’
#> Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
#> Also defined by ‘Rmpfr’
#> Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
#> Also defined by ‘Rmpfr’
#> Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
#> Also defined by ‘Rmpfr’
#> Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
#> Also defined by ‘Rmpfr’
#> Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
#> Also defined by ‘Rmpfr’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Finished HMP_2012_16S_gingival_V35_subset.
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’

aldex_res <- aldex_pq(gingival_pq,
  bifactor = "body_subsite",
  modalities = c("supragingival_plaque", "subgingival_plaque")
)
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> aldex.clr: generating Monte-Carlo instances and clr values
#> conditions vector supplied
#> operating in serial mode
#> aldex.scaleSim: adjusting samples to reflect scale uncertainty.
#> aldex.ttest: doing t-test
#> aldex.effect: calculating effect sizes

gg_aldex_plot(aldex_res, type = "volcano")

Usage

Arguments

Value

Details

See also

Examples