plot_gs_network: Visualise a network from a tidygraph object
In steveped/spBioUtils: Various utility functions for bioinformatics

Description Usage Arguments Details Value Examples

View source: R/plot_gs_network.R

Visualise a gene-expression network

plot_gs_network(
  tg,
  layout = "fr",
  up_col = "#FF000033",
  down_col = "#0000FF33",
  palette = "Dark2",
  palette_type = c("RColorBrewer", "grDevices"),
  gs_label_size = 3,
  gs_point_size = 10,
  gs_shape = 21,
  gs_label_repel = TRUE,
  gs_label_padding = unit(0.15, "lines"),
  gs_text_col = "black",
  gene_label_repel = TRUE,
  gene_shape = 21,
  gene_alpha = 0.7,
  gene_text_col = "black",
  stroke = 0.5,
  scale_size_trans = "sqrt",
  scale_size_range = c(1, 3.5),
  na_col = "grey80"
)

`tg`	The gene-set network as a tidygraph, as output by make_gs_network
`layout`	The layout algorithm to apply
`up_col`	The colour to label up-regulated genes
`down_col`	The colour to label down-regulated genes
`palette`	The name of the palette to use for gene-set nodes. Can be drawn from those provided in RColorBrewer::brewer.pal, or grDevices::hcl.colors
`palette_type`	Choose either RColorBrewer or grDevices palettes
`gs_label_size`	Size of gene-set labels
`gs_point_size`	Size of gene-set nodes
`gs_shape`	Shape to use for gene-set nodes
`gs_label_repel`	logical(1). Should the gene-set labels repel away from the points
`gs_label_padding`	Set the padding within each label around the text
`gs_text_col`	Text colour for node labels
`gene_label_repel`	logical(1). Should the gene labels repel away from the points
`gene_shape`	Shape to use for gene-level nodes
`gene_alpha`	Transparency of gene-level nodes
`gene_text_col`	Colour of the gene names
`stroke`	Controls thickness of the coloured region inside any point with a fill attribute
`scale_size_trans`	Passed to scale_size_continuous(trans = scale_size_trans)
`scale_size_range`	Passed to scale_size_continuous(range = scale_size_range)
`na_col`	The colour for any lines and points with missing values

Draws a network graph of genes connected to gene-sets. By default, up-regulated genes will be coloured red, whlst down-regulated genes will be coloured blue. This requires a column labelled 'logFC' to be included in the nodes component of the tidygraph.

It is also assumed that an NA value for logFC will be provided for the gene-set nodes. This is used to generate colours for each node, with edges from each node being drawn in the same colours, making this column mandatory

Available palettes for nodes can be found using rownames(RColorBrewer::brewer.pal.info) for the RColorBrewer palettes, or hcl.pals() for the grDevices palettes

A ggplot2 object

set.seed(100)
geneSets <- list(
  a = as.character(1:3), b = as.character(3:5), c = as.character((1:3)*2)
)
topTable <- tibble(
  gene_name = as.character(1:6), PValue = runif(6), logFC = runif(6, -3, 3)
)
tg <- make_gs_network(gene_sets = geneSets, top_table = topTable)
plot_gs_network(tg)
## Plots can be easily customised
suppressWarnings(
  plot_gs_network(tg, gs_shape = NA, gs_label_repel = FALSE,
  gs_label_size = 10, gs_label_padding = unit(0.5, "line")
  )
)