imprints_network: imprints_network

In mgerault/mineCETSAapp: A shiny app for IMPRINTS.CETSA package

imprints_network

Description

Function to plot an interactive STRING network with the IMPRINTS barplots in each nodes

Usage

imprints_network(
  data,
  hits = NULL,
  treatment = NULL,
  GOterm = NULL,
  required_score = 400,
  node_wolink = TRUE,
  witherrorbar = TRUE,
  FC_border = TRUE,
  colorbar = NULL,
  colorFC = c("#0041FF", "#FFFFFF", "#FF0000"),
  species = c("human", "mouse", "rat"),
  physics_type = c("forceAtlas2Based", "barnesHut", "repulsion", "hierarchicalRepulsion"),
  physics_enabled = TRUE,
  ...
)

Arguments

data	Dataset after imprints_caldiff
hits	The Uniprots ids from which you want to plot the network. If NULL, it will take all the proteins from the data.
treatment	The treatment from which you want to plot to plot the barplots. If NULL, it will plot all the treatments present in the data.
GOterm	Either a data frame containing the columns 'id', 'GOterm' and eventually 'color'; a character corresponding to a data base or a NULL object. If you choose a data base, it will perform an enrichment analysis and assign a GO term with the lowest FDR to each protein. The data bases now supported are: COMPARTMENTS, Process, Component, Function, TISSUES, Keyword, KEGG, SMART, PMID, RCTM, WikiPathway and NetworkNeighborAL
required_score	A numeric between 0 and 1000 to set the required score for the interaction in the STRING network.
node_wolink	Logical to tell if you want to print node without links in the network. Default set to TRUE
witherrorbar	Logical to tell if you want to print the error bar or not on the bar plots.
FC_border	Logical to tell if you want to color the nodes borders according to the maximum Fold-Change from each protein.
colorbar	A vector of colors corresponding to each treatment.
colorFC	If FC_border is set to TRUE, a vector of three color corresponding to the min, mid and max value from the maximum fold change.
species	The species; either human, mouse or rat.
physics_type	A string corresponding to the solver of the network; default is forceAtlas2Based. Possible options: 'barnesHut', 'repulsion', 'hierarchicalRepulsion', 'forceAtlas2Based'.
physics_enabled	Logical to toggle the physics system on or off.
...	Options for network visualization. Options available are: borderWidth, imagePadding, node_size, edge_length, edge_color font_background, font_color, legend_width, file_type

Value

visNetwork object

mgerault/mineCETSAapp documentation built on April 17, 2025, 7:24 p.m.