Plots the pathway with colored nodes and labels

Usage

plot_kegg_image_pathway(
  pathway,
  no_color_mode = T,
  mapping_data_type = "signal",
  log_norm = TRUE,
  use_old_images = FALSE,
  plot_type = "kegg",
  highlight_nodes = NULL,
  highlight_color = "red",
  adj = c(0.48, 1),
  y_adj_text = 0,
  y_adj_sink = 0
)

Arguments

pathway: list object from kegg collection
no_color_mode: when set to FALSE pathway nodes will be color coded with log expression FC values or log PSF values and color legend will be added to the pathway plot. Default value is TRUE
mapping_data_type: type on node values to bi visualized. Possible values c("signal", "exp").
log_norm: log transform PSF and expression values before color mapping. Default value is TRUE
use_old_images: use_old_images use olde kegg images(for use with curated pathway collection).
plot_type: network visualization type. Possible values c("kegg", "visnet"). When kegg option is used the bathway will be plotted over kegg png image. With visnet option function will plot interactive network with kegg layou.
highlight_nodes: single value of node id or a vector of ids to be highlighted in plotted pathway. Default value is NULL
highlight_color: Highlighed nodes color(s). Default values is "red"
adj: two values in between 0 and 1 which specify the x and y adjustment of the node labels, with 0 for left/bottom, 1 for right/top, and 0.5 for centered. Default value is c(0.48, 1). On most devices values outside 0 and 1 will also work. Only applicable for KEGG visualization type.
y_adj_text: Numeric value to adjust Y position of node labels. Depending on R version this value should be adjusted to have accurate text alignment. Default value is 0.
y_adj_sink: Numeric value to adjust Y position of sink node sign labels. Depending on R version this value should be adjusted to have accurate alignment. Default value is 0.