Plot a Graph on a Decoration — plot_dec

Plot with nodes only, edges only, or both (geometric graph) over a decoration image.

plot_dec_grph(nodes = NULL,
              edges = NULL,
              imgs,
              site,
              decor,
              dir = getwd(),
              nd.var = 'id',
              nd.color = 'orange',
              nd.size = 0.5,
              lbl.color = 'black',
              lbl.size = 0.5,
              ed.color = c("orange", "blue"),
              ed.lwd = 1,
              dir.out = dir,
              out.file.name = NULL,
              img.format = NULL,
              res = 300)

Arguments

nodes	Dataframe of nodes
edges	Dataframe of edges
imgs	Dataframe of decorations
site	Name of the site
decor	Name of the decoration
dir	Data folder including the decoration images. By default the working directory.
nd.var	Field name in the nodes data frame to be displayed as node labels. By default the identifier `nodes$id`.
nd.color, nd.size, lbl.color, lbl.size, ed.color, ed.lwd	Graphical parameters for color and size/widths of nodes, edges, and labels. `ed.color` is a vector with two values (the second value is used for diachronic edges).
dir.out	Folder for the output image. By default, it coincides with the input `dir`.
out.file.name	Name of the output image, including path from current directory and extension. By default the name is automatically generated including `site`, `decor`, `nd.var`, and the extension from `img.format`. If set, `out.file.name` overrides `dir.out` and `img.format`.
img.format, res	Format and resolution of the saved images. The handled formats are `"png"`, `"bmp"`, `"tiff"`/`"tif"`, `"jpeg"`/`"jpg"`, and `"pdf"`. The default resolution is 300 (ppi). The resolution does not applies to format pdf. if `img.format=NULL` (default), the plot is sent to the active device.

Details

Plot nodes only (if edges = NULL), edges only (if nodes = NULL), or both (graph) over a decoration image.

Value

Generates graph decoration images with nodes, edges, or both, overlapping the decoration image.

If img.format=NULL, the plot is sent to the active device and no value is returned.

If img.format= "png" or "bmp" or "tiff"/"tif" or "jpeg"/"jpg" or "pdf", the return value is a character vector with the dir/name of the saved image in the indicated format.

Examples

## Set data folder
dataDir <- system.file("extdata", package = "iconr")
## Decoration to be plotted
site <- "Brozas"
decor <- "Brozas"
## Read nodes, edges, and decorations
nds.df <- read_nds(site, decor, dataDir)
eds.df <- read_eds(site, decor, dataDir)
imgs <- read.table(paste0(dataDir, "/imgs.tsv"),
                   sep="\t", stringsAsFactors = FALSE)

## Plot 'Brozas' nodes and edges on the active device
## with node variable "type" as labels
plot_dec_grph(nds.df, eds.df, imgs,
              site, decor,
              dir = dataDir,
              lbl.size = 0.4,
              nd.var = "type")

## Save only edges of 'Brozas' with bigger widths and in image format jpg.
outDir <- tempdir()
img.filename <- plot_dec_grph(nodes = NULL, eds.df, imgs,
                              site, decor,
                              dir = dataDir,
                              ed.lwd = 2,
                              dir.out = outDir,
                              img.format = "jpg")
## Then read and plot the image.
a.dec <- magick::image_read(img.filename)

## Inspect the output image
magick::image_info(a.dec)
#> # A tibble: 1 x 7
#>   format width height colorspace matte filesize density
#>   <chr>  <int>  <int> <chr>      <lgl>    <int> <chr>  
#> 1 JPEG     734    826 sRGB       FALSE    70993 300x300

## Plot the output image
plot(a.dec)