Import introgression results — import

Import introgression summaries into a typed tidy object for use with plot_introgression() or ggpop() + geom_introgression().

Usage

import_introgression(
  dir = NULL,
  ...,
  type = c("auto", "dsuite_dtrios", "dsuite_dinvestigate", "fixed_diff",
    "genomics_general", "admixtools", "treemix", "qpgraph")
)

Arguments

dir: Directory containing introgression result files, or a single file path.
...: Optional named file paths. Relative paths are resolved inside dir.
type: Input type. Supports Dsuite Dtrios/BBAA/Dmin trio summaries, Dsuite Dinvestigate/localFstats window summaries, fixed-difference trio summaries, genomics_general ABBA-BABA window outputs, ADMIXTOOLS qpdstat/f3/f4ratio tables, TreeMix internal edge/treeout summaries, and legacy qpGraph edge tables. TreeMix *.edges.gz imports use matching *.vertices.gz files when present to recover the drift-coordinate layout.

Value

A ggpop_introgression tidy S3 data frame with standardized columns including analysis, stat, value, and format-specific columns such as chr, start, end, pop1, pop2, pop3, from, and to.

Details

Windowed Dsuite Dinvestigate/localFstats and genomics_general ABBA-BABA outputs are normalized to one row per statistic per window. Dsuite Dtrios/BBAA/Dmin files are imported as trio-level D statistic summaries. ADMIXTOOLS qpdstat, f3, and f4ratio outputs are imported as trio statistic tables. TreeMix internal *.edges.gz and *.treeout.gz files are imported as lightweight graph summaries. For *.edges.gz, a same-prefix *.vertices.gz file is used when available to add x, y, xend, and yend drift coordinates; *.treeout.gz alone remains a migration-edge summary. Legacy qpGraph edge tables expect user-facing from and to columns.

Examples

local_fstats <- system.file(
  "extdata", "introgression", "Dsuite",
  "PopB_PopC_PopA_localFstats_run1_100_50.txt",
  package = "ggPopi"
)
intro <- import_introgression(local_fstats, type = "dsuite_dinvestigate")
intro |> plot_introgression(stat = c("D", "fdM"))


trios <- import_introgression(
  system.file("extdata", "introgression", "Dsuite", "dsuite_results_BBAA.txt", package = "ggPopi"),
  type = "dsuite_dtrios"
)
trios |> plot_introgression(style = "matrix")


qpdstat <- import_introgression(
  system.file("extdata", "introgression", "admixtools", "qpdstat_result.csv", package = "ggPopi"),
  type = "admixtools"
)
qpdstat |> plot_introgression()