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 |
getGenesClassification |
get genes classification |
getListProfData |
get list of data frame with profiles data (CNA,mRNA, Methylation, Mutation...) |
getList_Cases |
get list of cases of each selected study in Classifier panel |
getList_GenProfs |
get list of genetic profiles of each selected study in Classifier panel |
getMegaProfData |
search and get genetic profiles (CNA,mRNA, Methylation, Mutation...) of gene list upper than 500 |
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 |