Write Plots to a PDF

Given a list of plots, write all plots to a single pdf file containing one plot per page, and optionally save the graph layout as a csv file.

Usage

saveNetworkPlots(
  plotlist,
  outfile,
  pdf_width = 12,
  pdf_height = 10,
  outfile_layout = NULL,
  verbose = FALSE
)

Arguments

plotlist

A named list whose elements are of class ggraph. May also contain an element named graph_layout with the matrix specifying the graph layout.

outfile

A connection or a character string containing the file path used to save the pdf.

pdf_width

Sets the page width. Passed to the width argument of pdf().

pdf_height

Sets the page height. Passed to the height argument of pdf().

outfile_layout

An optional connection or file path for saving the graph layout. Passed to the file argument of write(), which is called with ncolumns = 2.

verbose

Logical. If TRUE, generates messages about the tasks performed and their progress, as well as relevant properties of intermediate outputs. Messages are sent to stderr().

Value

Returns TRUE, invisibly.

References

Hai Yang, Jason Cham, Brian Neal, Zenghua Fan, Tao He and Li Zhang. (2023). NAIR: Network Analysis of Immune Repertoire. Frontiers in Immunology, vol. 14. doi: 10.3389/fimmu.2023.1181825

Webpage for the NAIR package

Author

Brian Neal (Brian.Neal@ucsf.edu)

Examples

set.seed(42)
toy_data <- simulateToyData()

net <-
  generateNetworkObjects(
    toy_data,
    "CloneSeq"
  )

net <-
  addPlots(
    net,
    color_nodes_by =
      c("SampleID", "CloneCount"),
    print_plots = TRUE
  )



saveNetworkPlots(
  net$plots,
  outfile =
    file.path(tempdir(), "network.pdf"),
  outfile_layout =
    file.path(tempdir(), "graph_layout.txt")
)

# Load saved graph layout
graph_layout <- matrix(
  scan(file.path(tempdir(), "graph_layout.txt"), quiet = TRUE),
  ncol = 2
)
all.equal(graph_layout, net$plots$graph_layout)
#> [1] "Mean relative difference: 8.87687e-08"


# \dontshow{
# clean up temporary directory
file.remove(
  file.path(tempdir(), c("network.pdf", "graph_layout.txt"))
)
#> [1] TRUE TRUE
# }