Interactive Multi-Omics Cancers Data Visualization and Analysis


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Documentation for package ‘bioCancer’ version 1.2.0

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bioCancer-package Launch bioCancer with default browser
attriColorGene Attribute Color to Gene
attriColorValue Attribute Color to Value
attriColorVector Attribute color to a vector of numeric values
attriShape2Gene Attribute shape to nodes
attriShape2Node Attributes shape to Nodes
bioCancer Launch bioCancer with default browser
checkDimensions Chech wich Cases and genetic profiles are available for every seleted study
coffeewheel This is an htmlwidgets-based visualization tool for hierarchical data. It is zoomable, meaning that you can interact with the hierarchy and zoom in/out accordingly.
coffeewheelOutput Widget output function for use in Shiny
displayTable Display dataframe in table using DT package
Edges_Diseases_obj get Edges dataframe for Gene/Disease association from geNetClassifier
getFreqMutData get mutation frequency
getListProfData get list of data frame with profiles data (CNA,mRNA, Methylation, Mutation...)
grepRef search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)
metabologram Circular plot of hierarchital data of genetic profile.
Mutation_obj Atribute mutation frequency to nodes
Node_df_FreqIn Attributes size to Nodes depending on number of interaction
Node_Diseases_obj Attributes color and shape to Nodes of Diseases
Node_obj_CNA_ProfData Attribute CNA data to node border
Node_obj_FreqIn Attribute interaction frequency to node size
Node_obj_Met_ProfData Attribute gene Methylation to Nodes
Node_obj_mRNA_Classifier Atrribute genes expression to color nodes
renderCoffeewheel Widget render function for use in Shiny
reStrColorGene Restructure the list of color attributed to the genes in every dimenssion for every studies
reStrDimension Restructure the list of color attributed to the genes in every study for every dimensions
reStrDisease Restructure the list of color attributed to the genes in every disease
sampleWheelData Sample data for wheel initialization
Studies_obj get object for grViz. Link Studies to genes
UnifyRowNames Unify row names in data frame with the same order of gene list.
whichGeneList Verify which gene list is selected