chordDiagramR: Build a chord diagram of duplicate occurrence links

In BeeBDC: Occurrence Data Cleaning

Build a chord diagram of duplicate occurrence links

Description

This function outputs a figure which shows the relative size and direction of occurrence points duplicated between data providers, such as, SCAN, GBIF, ALA, etc. This function requires the outputs generated by dupeSummary().

Usage

chordDiagramR(
  dupeData = NULL,
  outPath = NULL,
  fileName = NULL,
  width = 7,
  height = 6,
  bg = "white",
  smallGrpThreshold = 3,
  title = "Duplicated record sources",
  palettes = c("cartography::blue.pal", "cartography::green.pal",
    "cartography::sand.pal", "cartography::orange.pal", "cartography::red.pal",
    "cartography::purple.pal", "cartography::brown.pal"),
  canvas.ylim = c(-1, 1),
  canvas.xlim = c(-0.6, 0.25),
  text.col = "black",
  legendX = grid::unit(6, "mm"),
  legendY = grid::unit(18, "mm"),
  legendJustify = c("left", "bottom"),
  niceFacing = TRUE,
  self.link = 2
)

Arguments

dupeData	A tibble or data frame. The duplicate file produced by dupeSummary().
outPath	Character. The path to a directory (folder) in which the output should be saved.
fileName	Character. The name of the output file, ending in '.pdf'.
width	Numeric. The width of the figure to save (in inches). Default = 7.
height	Numeric. The height of the figure to save (in inches). Default = 6.
bg	The plot's background colour. Default = "white".
smallGrpThreshold	Numeric. The upper threshold of sub-dataSources to be listed as "other". Default = 3.
title	A character string. The figure title. Default = "Duplicated record sources".
palettes	A vector of the palettes to be used. One palette for each major dataSource and "other" using the paletteer package. Default = c("cartography::blue.pal", "cartography::green.pal", "cartography::sand.pal", "cartography::orange.pal", "cartography::red.pal", "cartography::purple.pal", "cartography::brown.pal")
canvas.ylim	Canvas limits from circlize::circos.par(). Default = c(-1.0,1.0).
canvas.xlim	Canvas limits from circlize::circos.par(). Default = c(-0.6, 0.25).
text.col	A character string. Text colour
legendX	The x position of the legends, as measured in current viewport. Passed to ComplexHeatmap::draw(). Default = grid::unit(6, "mm").
legendY	The y position of the legends, as measured in current viewport. Passed to ComplexHeatmap::draw(). Default = grid::unit(18, "mm").
legendJustify	A character vector declaring the justification of the legends. Passed to ComplexHeatmap::draw(). Default = c("left", "bottom").
niceFacing	TRUE/FALSE. The niceFacing option automatically adjusts the text facing according to their positions in the circle. Passed to circlize::highlight.sector().
self.link	1 or 2 (numeric). Passed to circlize::chordDiagram(): if there is a self link in one sector, 1 means the link will be degenerated as a 'mountain' and the width corresponds to the value for this connection. 2 means the width of the starting root and the ending root all have the width that corresponds to the value for the connection.

Value

Saves a figure to the provided file path.

Examples

## Not run: 
  # Create a basic example dataset of duplicates to visualise
basicData <- dplyr::tribble(
                            ~dataSource,    ~dataSource_keep,
                      "GBIF_Halictidae",         "USGS_data",
                      "GBIF_Halictidae",         "USGS_data",
                      "GBIF_Halictidae",         "USGS_data",
                      "GBIF_Halictidae",         "USGS_data",
                      "GBIF_Halictidae",         "USGS_data",
                      "GBIF_Halictidae",         "USGS_data",
                      "SCAN_Halictidae",   "GBIF_Halictidae",
                   "iDigBio_halictidae",   "GBIF_Halictidae",
                   "iDigBio_halictidae",   "SCAN_Halictidae",
                   "iDigBio_halictidae",   "SCAN_Halictidae",
                      "SCAN_Halictidae",   "GBIF_Halictidae",
                       "iDigBio_apidae",       "SCAN_Apidae",
                          "SCAN_Apidae",    "Ecd_Anthophila",
                       "iDigBio_apidae",    "Ecd_Anthophila",
                          "SCAN_Apidae",    "Ecd_Anthophila",
                       "iDigBio_apidae",    "Ecd_Anthophila",
                    "SCAN_Megachilidae", "SCAN_Megachilidae",
                      "CAES_Anthophila",   "CAES_Anthophila",
                      "CAES_Anthophila",   "CAES_Anthophila"
 )


 chordDiagramR(
dupeData = basicData,
outPath = tempdir(),
fileName = "ChordDiagram.pdf",
# These can be modified to help fit the final pdf that's exported.
width = 9,
height = 7.5,
bg = "white",
# How few distinct dataSources should a group have to be listed as "other"
smallGrpThreshold = 3,
title = "Duplicated record sources",
# The default list of colour palettes to choose from using the paleteer package
palettes = c("cartography::blue.pal", "cartography::green.pal", 
             "cartography::sand.pal", "cartography::orange.pal", "cartography::red.pal",
             "cartography::purple.pal", "cartography::brown.pal"),
canvas.ylim = c(-1.0,1.0), 
canvas.xlim = c(-0.6, 0.25),
text.col = "black",
legendX = grid::unit(6, "mm"),
legendY = grid::unit(18, "mm"),
legendJustify = c("left", "bottom"),
niceFacing = TRUE)
## End(Not run)

BeeBDC documentation built on Nov. 4, 2024, 9:06 a.m.