plot_features: Get a network of features of interest from STRING website

In chiasinL/STRINGutils: Additional utilities for STRINGdb

Description

plot_features gets the STRING network or subnetwork of features of interests and save as a SVG file.

Usage

plot_features(
  df_mapped,
  colors_vec,
  string_db,
  network_flavor = c("evidence", "confidence", "actions"),
  n_hits = 200,
  entire = FALSE,
  get_ann = FALSE
)

Arguments

df_mapped	A data frame. Mapped data frame generated by STRINGdb's method map.
colors_vec	A named character vector of colors for feature of interest.
string_db	An instantiated STRINGdb reference class. See STRINGdb-class.
network_flavor	One of "evidence", "confidence", "actions", specify the flavor of the network
n_hits	Integer. The number of nodes to get from STRING network.
entire	Logical. Return the entire STRING network if TRUE. Only clusters contain features of interest are returned if FALSE.
get_ann	Logical. Add annotations to the table of features of interest.

Value

Return a SVG file of network of features of interest.

Examples

## Not run: 
feature_of_int <- c("VSTM2L", "TBC1D2", "LENG9", "TMEM27", "TSPAN1",
 "TNNC1", "MGAM","TRIM22","KLK11", "TYROBP")
colors_vec <- rep("rgb(101,226,11)", length(feature_of_int))
names(colors_vec) <- feature_of_int

plot_features(example1_mapped, colors_vec, string_db, n_hits = 500, entire = TRUE, get_ann = TRUE)
s
plot_features(example1_mapped, colors_vec, string_db, get_ann = TRUE)

## End(Not run)

chiasinL/STRINGutils documentation built on Dec. 19, 2021, 3:56 p.m.