ggMap_Connectivity: Create a 'ggplot2' map object of a connectivity matrix
In wStockhausen/rDisMELS: Basic functions for dealing with DisMELS IBM model output

ggMap_Connectivity

R Documentation

Create a ggplot2 map object of a connectivity matrix

Description

Function to create a ggplot2 map object of a connectivity matrix.

Usage

ggMap_Connectivity(
  tbl_conn,
  tbl_web,
  bmls = NULL,
  maxVal = NA,
  valCol = "value",
  facetGrid = NULL,
  facetWrap = NULL,
  facetByRow = TRUE,
  nrow = NULL,
  ncol = NULL,
  label = "value",
  val_min = 0,
  bin_size = NULL,
  bin_max = NULL,
  max_size = 3,
  linewidth = NA,
  alpha = NA,
  reverse = TRUE,
  scale_colour = ggplot2::scale_colour_viridis_c(option = "plasma", limits = c(0,
    maxVal), oob = scales::squish),
  scale_size = ggplot2::scale_size_area(max_size = max_size, oob = scales::squish),
  scale_alpha = ggplot2::scale_alpha_continuous(oob = scales::squish),
  arrow = grid::arrow(20, grid::unit(0.15, "inches")),
  noAxisLabels = TRUE,
  plotRetentionOnly = FALSE,
  plotExportedOnly = FALSE
)

Arguments

`tbl_conn`	- tibble with connectivity values to plot
`tbl_web`	- tibble representing the connectivity web
`bmls`	- list of base map layers ggplot2 layer objects
`maxVal`	- max value for scales (higher values will be set to maxVal)
`valCol`	- column name for values to plot
`facetGrid`	- formula for faceting variables using `ggplot2::facet_grid`
`facetWrap`	- column name(s) for faceting variable(s) using `ggplot2::facet_wrap`
`facetByRow`	- flag (T/F) to arrange facets by row
`nrow`	- number of rows to arrange facets in (if facetByRow is TRUE)
`ncol`	- number of columns to arrange facets in (if facetByRow is FALSE)
`label`	- label for legends
`val_min`	- minimum value to include (0 is never included)
`bin_size`	- bin size (no binning if NULL)
`bin_max`	- max bin value, if binning applied
`max_size`	- max size for connectivity arrows
`linewidth`	- line width for fixed-width arrows
`alpha`	- transparency value for fixed-alpha symbols and arrows
`reverse`	- plot connections in reverse order (largest on bottom)
`scale_colour`	- ggplot2 colour scale for connectivity values (default = ggplot2::scale_colour_viridis_c(option="plasma",limits=c(0,maxVal)))
`scale_size`	- ggplot2 size scale for connectivity values (default = scale_size_area(max_size=max_size,oob=scales::squish))
`scale_alpha`	- ggplot2 transparency scale for connectivity values (default = scale_alpha_continuous(oob=scales::squish))
`arrow`	- pass result from call to `arrow`
`noAxisLabels`	- flag (T/F) to include axis labels
`plotRetentionOnly`	- flag (T/F) to plot only retained proportions
`plotExportedOnly`	- flag (T/F) to plot only non-retained (exported) proportions