Draw a network on PPI result — PPInetwork • DEP2

Draw a network on PPI result output from test_PPI

Usage

PPInetwork(
  PPIlinks,
  layoutway = "layout_components",
  nodecolor = "#2EA9DF",
  nodeshape = c("circle", "square"),
  linecolor = "#ADD8E6",
  nodesize = 20,
  changesize = FALSE,
  fontsize = 25,
  changewidth = FALSE,
  linewidth = 5,
  smoothline = FALSE,
  smoothtype = "continous",
  highlightkey = TRUE,
  returntype = c("visNetwork", "igraph")
)

Arguments

PPIlinks: The PPI result from test_ppi
layoutway: Character(1), the name of a layout function in igraph package,such as "layout_as_star", "layout_as_tree", "layout_in_circle". See layout.
nodecolor: Character(1), the color of node.
nodeshape: Character(1), the shape of node. One of "circle", "square", "raster", or other vertex.shapes in igraph.
linecolor: Character(1), the color of edge line.
nodesize: Numeric(1), the size of node.
changesize: Logical(1), whether change node size by link number.
fontsize: Numeric(1), the font size of label.
changewidth: Logical(1), whether change edge width by interaction score.
linewidth: Numeric(1), the width of edge.
smoothline: Logical(1), whether smooth the edge. Works only for visNetwork
smoothtype: Character(1), one of 'dynamic', 'continuous', 'discrete', 'diagonalCross', 'straightCross', 'horizontal', 'vertical', 'curvedCW', 'curvedCCW', 'cubicBezier'
highlightkey: logical(1), whether label the central nodes by red which have at least 6 interactions.
returntype: Character(1), "visNetwork" or "igraph".

Value

A visNetwork plot or a igraph obejct according returntype.

Examples

if (FALSE) {
# Load example
data(Silicosis_pg)
data <- Silicosis_pg
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

# Differential test
ecols <- grep("LFQ.", colnames(data_unique))
se <- make_se_parse(data_unique, ecols,mode = "delim")
filt <- filter_se(se, thr = 0, fraction = 0.4, filter_formula = ~ Reverse != "+" & Potential.contaminant!="+")
norm <- normalize_vsn(filt)
imputed <- impute(norm, fun = "MinProb", q = 0.05)
diff <- test_diff(imputed, type = "control", control  = c("PBS"), fdr.type = "Storey's qvalue")
dep <- add_rejections(diff, alpha = 0.01,lfc = 2)

# PPI construct
if(check_PPI_depends()){

  # Load STRING data. If local STRING is missing, PPI_res will download to system.file("PPIdata", "Mouse",package = "DEP2")
  load_PPIdata(speciesname = "Mouse")

  PPI_res <- test_PPI(dep, contrasts = "W4_vs_PBS", species = "Mouse",
                      STRING.version = "11.5",score_cutoff = 400)

  ## igraph network
  PPI_ig <- PPInetwork(PPI_res, returntype = "igraph")
  igraph::plot.igraph(PPI_ig)

  ## visNetwork network
  PPInetwork(PPI_res, returntype = "visNetwork")
  }
}