Plot significantly perturbed gene-sets as a network

Plot significantly perturbed gene-sets as a network

plot_gs_network(
  normalisedScores,
  gsTopology,
  colorBy = NULL,
  foldGSname = TRUE,
  foldafter = 2,
  layout = c("fr", "dh", "gem", "graphopt", "kk", "lgl", "mds", "sugiyama"),
  edgeAlpha = 0.8,
  edgeWidthScale = c(0.5, 3),
  edgeLegend = FALSE,
  nodeSizeScale = c(3, 6),
  nodeShape = 16,
  showLegend = TRUE,
  gsLegTitle = NULL,
  gsNameSize = 3,
  gsNameColor = "black",
  plotIsolated = FALSE,
  maxOverlaps = 10,
  ...
)

Arguments

normalisedScores

A data.frame of pathway perturbation scores derived from the normalise_by_permu() function

gsTopology

List of pathway topology matrices generated using function retrieve_topology()

colorBy

Choose to color nodes either by robustZ or pvalue. A column must exist in the normalisedScores data.frame for the chosen parameter

foldGSname

logical(1) Should long gene-set names fold across multiple lines

foldafter

The number of words after which gene-set names should be folded. Defaults to 2

layout

The layout algorithm to apply. Accept all layout supported by igraph

edgeAlpha

numeric(1) Transparency of edges. Default to 0.8

edgeWidthScale

A numerical vector of length 2 to be provided to ggraph::scale_edge_width_continuous() for specifying the minimum and maximum edge widths after transformation. Defaults to c(0.5, 3)

edgeLegend

logical(1) Should edge weight legend be shown

nodeSizeScale

A numeric vector of length 2 to be provided to ggplot2::scale_size() for specifying the minimum and maximum node sizes after transformation. Defaulted to c(3,6)

nodeShape

Shape of nodes

showLegend

logical(1) Should color legend be shown

gsLegTitle

Optional title for the color legend

gsNameSize

Size of node text labels

gsNameColor

Color of node text labels

plotIsolated

logical(1) Should nodes not connected to any other nodes be plotted. Defaults to FALSE

maxOverlaps

passed to geom_node_text

...

Not used

Value

A ggplot2 object

Examples

load(system.file("extdata", "gsTopology.rda", package = "sSNAPPY"))
load(system.file("extdata", "normalisedScores.rda", package = "sSNAPPY"))

# Subset pathways significantly perturbed in sample R5020_N2_48
subset <- dplyr::filter(
  normalisedScores, adjPvalue < 0.05, sample == "R5020_N2_48"
)
subset[["status"]] <- ifelse(subset[["robustZ"]]> 0, "Activated", "Inhibited")


# Color network plot nodes by status
plot_gs_network(subset, gsTopology,
colorBy = "status", layout = "dh",
gsLegTitle = "Direction of pathway Perturbation")


# Color network plot nodes by p-values
plot_gs_network(subset, gsTopology, layout = "dh",
colorBy = "pvalue", gsLegTitle = "P-value")