X.local.network — X.local.network • MAPX

Calculate and plot a local subnetwork of a specific protein or proteins of interest.

Usage

X.local.network(
  data = c(),
  proteins = c(),
  cutoff = 0.5,
  scores.col = NA,
  condition.col = NA,
  min.conditions = 1,
  plot = NULL,
  plot.annotation = NULL,
  plot.design.params = list(),
  plot.cytoscape.path = NA,
  plot.cytoscape.waittime = 40,
  plot.name = paste(proteins, collapse = "_"),
  plot.path = "./"
)

Arguments

data: Data frame with columns for protein1, protein2 and a column with scores
proteins: Vector: proteins whose local network should be plotted.
cutoff: Numeric: Probabilities cutoff applied to the data.
scores.col: Character string: Name of the columns with prediction values.
condition.col: Character string: If the data has more conditions, what is the name of the column containing conditions?
min.conditions: Numeric: At least how many conditions must contain the predicted interaction to not be filtered out?
plot: Character string: "cytoscape" for plotting using cytoscape and "visnetwork" for plotting using visNetwork package. NULL for no plotting.
plot.annotation: Data frame with column 'id' with protein IDs and any other annotation columns.
plot.design.params: List: as design.params in X.plot.network.
plot.cytoscape.path: String: As in X.plot.network.
plot.cytoscape.waittime: Numeric: How many second should R wait for the cytoscape to start.
plot.name: String: Plot name for saved cytoscape network.
plot.path: String: Output destination for the plot.

Value

A data frame with network edges.

Examples

local.subnetwork <- X.local.network(calibrated.model$data%>%dplyr::select(!score),"PF3D7_0412200",
            plot="cytoscape",
            plot.annotation=plasmoDB_data%>%dplyr::rename(protein=Accession),
            plot.cytoscape.path="C://Program Files/Cytoscape_v3.9.1/Cytoscape.exe")
#> Error in calibrated.model$data %>% dplyr::select(!score): could not find function "%>%"