clinesXenvironment: Function to correlate INTROGRESS genomic clines with raster...

In btmartin721/ClineHelpR: Parses and Plots BGC and INTROGRESS Output

Function to correlate INTROGRESS genomic clines with raster data

Description

Function to correlate INTROGRESS genomic clines with raster data

Usage

clinesXenvironment(
  clineList,
  rasterPointValues,
  rastersToUse = NULL,
  clineLabels = c("P1, Het", "P2"),
  outputDIR = "./plots",
  showPLOTS = FALSE,
  clineMethod = "permutation",
  prefix = "population1",
  cor.method = "auto"
)

Arguments

clineList	List object returned from runIntrogress
rasterPointValues	List of data.frames with raster values at each sample locality. See ?extractPointValues
rastersToUse	Integer vector indicating which raster layers to use for genomic cline X environment plots. If NULL, uses all rasters
clineLabels	Character vector of length == 3 designating population names for c(P1, Het, P2)
outputDIR	File path to directory for outputting plots
showPLOTS	Boolean; Whether to print the plots to the screen
clineMethod	Character string indicating desired method for generating genomic clines. Must be either "permutation" or "parametric". See ?introgress
prefix	Character prefix for output files
cor.method	Method for correlations c("pearson", "kendall", "spearman)
sample.info	File path to sample info file with 4 columns: indID,popID,latitude,longitude
header	Boolean specifying if sample.info has a header line
coords	data.frame with coordinates. Can be taken from env.list, an object returned from the prepare_rasters() function. See ?prepare_rasters(). If used, value is env.list[3]

Examples

clinesXenvironment(clineList = eatt,
                   rasterPointValues = rasterPoints,
                   rasterToUse = NULL,
                   clineLabels = c("EA", "Het", "TT"),
                   outputDIR = "./cline_plots",
                   clineMethod = "permutation",
                   prefix = "eatt",
                   cor.method = "auto")

btmartin721/ClineHelpR documentation built on Oct. 15, 2024, 5:05 a.m.