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R/StyleMappings.R

R/StyleMappings.R
In cytoscape/RCy3: Functions to Access and Control Cytoscape

Defines functions .genShapeMap .genArrowMap .genLineStyleMap .genDimMap .genOpacityMap .genColorMap .autoTableColumnValues paletteColorVirdis paletteColorBrewerBrBG paletteColorBrewerPiYG paletteColorBrewerPRGn paletteColorBrewerPuOr paletteColorBrewerRdBu paletteColorBrewerRdYlBu paletteColorBrewerBlues paletteColorBrewerBuGn paletteColorBrewerBuPu paletteColorBrewerGnBu paletteColorBrewerGreens paletteColorBrewerGreys paletteColorBrewerOranges paletteColorBrewerOrRd paletteColorBrewerPuBu paletteColorBrewerPuBuGn paletteColorBrewerPuRd paletteColorBrewerPurples paletteColorBrewerRdPu paletteColorBrewerReds paletteColorBrewerYlGn paletteColorBrewerYlGnBu paletteColorBrewerYlOrBr paletteColorBrewerYlOrRd paletteColorBrewerSet3 paletteColorBrewerSet2 paletteColorBrewerSet1 paletteColorBrewerPaired paletteColorBrewerAccent paletteColorBrewerDark2 paletteColorBrewerPastel1 paletteColorBrewerPastel2 paletteColorRandom setEdgeSourceArrowShapeMapping setEdgeTargetArrowShapeMapping setEdgeLabelOpacityMapping setEdgeFontFaceMapping setNodeLabelOpacityMapping setNodeFontFaceMapping setNodeFillOpacityMapping setNodeBorderOpacityMapping getAllStyleMappings getStyleMapping deleteStyleMapping updateStyleMapping mapVisualProperty

Documented in deleteStyleMapping getAllStyleMappings getStyleMapping mapVisualProperty paletteColorBrewerAccent paletteColorBrewerBlues paletteColorBrewerBrBG paletteColorBrewerBuGn paletteColorBrewerBuPu paletteColorBrewerDark2 paletteColorBrewerGnBu paletteColorBrewerGreens paletteColorBrewerGreys paletteColorBrewerOranges paletteColorBrewerOrRd paletteColorBrewerPaired paletteColorBrewerPastel1 paletteColorBrewerPastel2 paletteColorBrewerPiYG paletteColorBrewerPRGn paletteColorBrewerPuBu paletteColorBrewerPuBuGn paletteColorBrewerPuOr paletteColorBrewerPuRd paletteColorBrewerPurples paletteColorBrewerRdBu paletteColorBrewerRdPu paletteColorBrewerRdYlBu paletteColorBrewerReds paletteColorBrewerSet1 paletteColorBrewerSet2 paletteColorBrewerSet3 paletteColorBrewerYlGn paletteColorBrewerYlGnBu paletteColorBrewerYlOrBr paletteColorBrewerYlOrRd paletteColorRandom paletteColorVirdis setEdgeFontFaceMapping setEdgeLabelOpacityMapping setEdgeSourceArrowShapeMapping setEdgeTargetArrowShapeMapping setNodeBorderOpacityMapping setNodeFillOpacityMapping setNodeFontFaceMapping setNodeLabelOpacityMapping updateStyleMapping 

# ==============================================================================
# Functions for defining MAPPINGS between table column values and visual 
# properties, organized into sections:
#
# I.   General functions for creating and applying mappings for node, edge and 
#      network properties
# II.  Specific functions for defining particular node, edge and network 
#      properties
# III. Functions for generating and mapping property values to colors, 
#      opacities, sizes, heights, widths and shapes
#
# ==============================================================================
# I. General Functions
# ------------------------------------------------------------------------------
#' Creates a mapping between an attribute and a visual property
#'
#' @description Generates the appropriate data structure for the "mapping" parameter
#' in updateStyleMapping.
#' @details The paired list of values must be of the same length or mapping will fail.
#' For gradient mapping, you may include two additional visual.prop.values in the 
#' first and last positions to map respectively to values less than and greater 
#' than those specified in table.column.values. Mapping will also fail if the 
#' data type of table.column.values does not match that of the existing table.column. 
#' Note that all imported numeric data are stored as Integers or Doubles in 
#' Cytosacpe tables; and character or mixed data are stored as Strings.
#' @param visual.prop (char) name of visual property to map
#' @param table.column (char) name of table column to map
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p)
#' @param table.column.values (list) list of values paired with visual.prop.values; skip for passthrough mapping
#' @param visual.prop.values (list) list of values paired with table.column.values; skip for passthrough mapping
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return (network=network, base.url=base.url) ready to convert into JSON by style mapping operations
#' @seealso updateStyleMapping getVisualPropertyNames
#' @examples
#' \donttest{
#' mapVisualProperty('node fill color','score','c',c(-4.0,0.0,9.0),c('#99CCFF','#FFFFFF','#FF7777'))
#' mapVisualProperty('node shape','type','d',c('protein','metabolite'),c('ellipse','rectangle'))
#' mapVisualProperty('node label','alias','p')
#' }
#' @section List of visual properties:
#' \tabular{lll}{
#' Node Border Stroke \tab Edge Bend \tab Network Background Paint \cr
#' Node Border Paint \tab Edge Curved \tab Network Center X Location \cr
#' Node Border Transparency \tab Edge Label \tab Network Center Y Location \cr
#' Node Border Width \tab Edge Label Color \tab Network Center Z Location \cr
#' Node CustomGraphics 1-9 \tab Edge Label Font Face \tab Network Depth \cr
#' Node CustomGraphics Position 1-9 \tab Edge Label Font Size \tab Network Edge Selection \cr
#' Node CustomGraphics Size 1-9 \tab Edge Label Transparency \tab Network Height \cr
#' Node CustomPaint 1-9 \tab Edge Label Width \tab Network Node Selection \cr
#' Node Depth \tab Edge Line Type \tab Network Scale Factor \cr
#' Node Fill Color \tab Edge Paint \tab Network Size \cr
#' Node Height \tab Edge Selected \tab Network Title \cr
#' Node Label \tab Edge Selected Paint \tab Network Width \cr
#' Node Label Color \tab Edge Source Arrow Selected Paint \tab  \cr
#' Node Label Font Face \tab Edge Source Arrow Shape \tab  \cr
#' Node Label Font Size \tab Edge Source Arrow Size \tab  \cr
#' Node Label Position \tab Edge Source Arrow Unselected Paint \tab  \cr
#' Node Label Transparency \tab Edge Stroke Selected Paint \tab  \cr
#' Node Label Width \tab Edge Stroke Unselected Paint \tab  \cr
#' Node Network Image Visible \tab Edge Target Arrow Selected Paint \tab  \cr
#' Node Paint \tab Edge Target Arrow Shape \tab  \cr
#' Node Selected \tab Edge Target Arrow Size \tab  \cr
#' Node Selected Paint \tab Edge Target Arrow Unselected Paint \tab  \cr
#' Node Shape \tab Edge Tooltip \tab  \cr
#' Node Size \tab Edge Transparency \tab  \cr
#' Node Tooltip \tab Edge Unselected Paint \tab  \cr
#' Node Transparency \tab Edge Visible \tab  \cr
#' Node Visible \tab Edge Visual Property \tab  \cr
#' Node Width \tab Edge Width \tab  \cr
#' Node X Location \tab  \tab  \cr
#' Node Y Location \tab  \tab  \cr
#' Node Z Location \tab  \tab  \cr
#' }
#' @export
mapVisualProperty <- function(visual.prop, table.column, mapping.type, table.column.values,
                              visual.prop.values, network=NULL, base.url=.defaultBaseUrl){
    
    suid <- getNetworkSuid(network,base.url)
    
    #process mapping type
    mapping.type.name = switch(mapping.type, 'c'='continuous','d'='discrete','p'='passthrough',mapping.type)
    
    #processs visual property, including common alternatives for vp names :)
    visual.prop.name = toupper(gsub("\\s+","_",visual.prop))
    visual.prop.name = switch(visual.prop.name,
                              'EDGE_COLOR'='EDGE_UNSELECTED_PAINT',
                              'EDGE_THICKNESS'='EDGE_WIDTH',
                              'NODE_BORDER_COLOR'='NODE_BORDER_PAINT',
                              'NODE_BORDER_LINE_TYPE'='NODE_BORDER_STROKE',
                              visual.prop.name)
    
    #check visual prop name
    if(!visual.prop.name %in% getVisualPropertyNames(base.url = base.url)){
        stop(paste0('Could not find ',visual.prop.name,
                     '. Run getVisualPropertyNames() to retrieve property names.'))
    }
    
    #check mapping column and get type
    tp = tolower(strsplit(visual.prop.name,"_")[[1]][1])
    table = paste0('default',tp)
    res <- cyrestGET(paste('networks',suid,'tables',table,'columns',sep='/'),base.url=base.url)
    table.column.type = NULL
    for(i in seq_len(length(res))){
        if(res[[i]]$name==table.column){
            table.column.type = res[[i]]$type
            break
        }
    }
    if(is.null(table.column.type))
        stop(paste0('Could not find ',table.column,' column in ',table,' table.'))
    
    #construct visual property map
    visual.prop.map <- list(
        mappingType=mapping.type.name,
        mappingColumn=table.column,
        mappingColumnType=table.column.type,
        visualProperty=visual.prop.name
    )
    
    if(mapping.type.name=='discrete'){
        map <- list()
        for (i in seq_len(length(table.column.values))) {
            map[[i]] <- list(key=toString(table.column.values[i]), value=toString(visual.prop.values[i]))
        }
        visual.prop.map$map=map
    }else if(mapping.type.name=='continuous'){
        points <- list()
        #check for extra lesser and greater values
        propValCount <- length(visual.prop.values)
        colValCount <- length(table.column.values)
        if (propValCount-colValCount == 2){
            for (i in seq_len(colValCount)) {
                points[[i]] <- list(value=table.column.values[i],
                                    lesser=visual.prop.values[i+1],
                                    equal=visual.prop.values[i+1], 
                                    greater=visual.prop.values[i+1]) #note offset
            }
            #then correct extreme values
            points[[1]] <- list(value=table.column.values[1],
                                lesser=visual.prop.values[1],
                                equal=visual.prop.values[2], 
                                greater=visual.prop.values[2]) 
            points[[colValCount]] <- list(value=table.column.values[colValCount],
                                          lesser=visual.prop.values[colValCount+1],
                                          equal=visual.prop.values[colValCount+1], 
                                          greater=visual.prop.values[colValCount+2]) 
        }
        else if (propValCount-colValCount == 0) {
            for (i in seq_len(colValCount)) {
                points[[i]] <- list(value=table.column.values[i],
                                    lesser=visual.prop.values[i],
                                    equal=visual.prop.values[i],
                                    greater=visual.prop.values[i])
            }
        }
        else {
            stop ("Table.column.values and visual.prop.values don't match up.")
        }
        visual.prop.map$points=points
    }
    return(visual.prop.map)
}

# ------------------------------------------------------------------------------
#' Updates a visual property mapping in a style
#'
#' @description Updates the visual property mapping, overriding any prior mapping. Creates a
#' visual property mapping if it doesn't already exist in the style.
#' @details Requires visual property mappings to be previously created, see mapVisualProperty.
#' @param style.name (char) name for style
#' @param mapping a single visual property mapping, see mapVisualProperty
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return server response
#' @export
#' @seealso mapVisualProperty
#' @examples
#' \donttest{
#' updateStyleMapping('myStyle',mapVisualProperty('node label','name','p'))
#' }
updateStyleMapping <- function(style.name, mapping, base.url=.defaultBaseUrl){
    visual.prop.name = mapping$visualProperty
    # set default style
    if(is.null(style.name)){
        style.name <- 'default'
        message('style.name not specified, so updating "default" style.')
    }
    # check if vp exists already
    res <- cyrestGET(paste('styles', style.name,'mappings',sep = '/')
                     ,base.url=base.url)
    vp.list <- lapply(res, function(x) unname(x['visualProperty'][[1]]))
    if(visual.prop.name %in% vp.list){
        exists = TRUE
    } else {
        exists = FALSE
    }
    
    if(exists==TRUE){     
        res <- invisible(cyrestPUT(paste('styles', style.name,'mappings',visual.prop.name, sep = '/'),
                            body=list(mapping), 
                            base.url=base.url))
    }
    else {   
        res <- invisible(cyrestPOST(paste('styles', style.name,'mappings',sep = '/'),
                             body=list(mapping), 
                             base.url=base.url))
    }
    Sys.sleep(get(".MODEL_PROPAGATION_SECS", envir=RCy3env)) ## NOTE: TEMPORARY SLEEP "FIX" 
    return(res)
}

# ------------------------------------------------------------------------------
#' @title Delete Style Mapping
#'
#' @description Deletes a specified visual style mapping from specified style.
#' @param style.name (char) name for style
#' @param visual.prop (char) name of visual property to map. 
#' See getVisualPropertyNames().
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' deleteStyleMapping()
#' }
#' @export
deleteStyleMapping<-function(style.name, visual.prop,  base.url=.defaultBaseUrl){
    # check if vp exists already
    res <- cyrestGET(paste('styles', style.name,'mappings',sep = '/')
                     ,base.url=base.url)
    vp.list <- lapply(res, function(x) unname(x['visualProperty'][[1]]))
    if(visual.prop %in% vp.list){
        exists = TRUE
    } else {
        exists = FALSE
    }
    
    if(exists==TRUE){     
        invisible(cyrestDELETE(paste('styles', style.name,'mappings',visual.prop, sep = '/'),
                            base.url=base.url))
    }
}

# ------------------------------------------------------------------------------
#' @title Get Style Mapping
#'
#' @description Retrieve the values the define the mappings for a given
#' visual property in a style.
#' @param visual.prop Name of the visual property, e.g., NODE_FILL_COLOR
#' @param style.name Name for style; default is the 'default' style
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is 
#' http://localhost:1234 and the latest version of the CyREST API supported by 
#' this version of RCy3.
#' @return List of named values defining the visual property mappings
#' @examples \donttest{
#' getStyleMapping()
#' }
#' @seealso getVisualPropertyNames
#' @export
getStyleMapping <- function(visual.prop, style.name=NULL,
                            base.url=.defaultBaseUrl){
    if(is.null(style.name)){
        style.name <- 'default'
        message('style.name not specified, so using "default" style.')
    }
    
    cyrestGET(paste('styles',style.name,'mappings', visual.prop, sep = '/'), 
              base.url=base.url)
}

# ------------------------------------------------------------------------------
#' @title Get All Style Mappings
#'
#' @description Retrieve the values the define all the mappings per visual 
#' property in a given style.
#' @param style.name Name for style; default is the 'default' style
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is 
#' http://localhost:1234 and the latest version of the CyREST API supported by 
#' this version of RCy3.
#' @return List of lists with named values defining the visual property mappings
#' @examples \donttest{
#' getStyleMapping()
#' }
#' @export
getAllStyleMappings <- function(style.name=NULL,
                            base.url=.defaultBaseUrl){
    if(is.null(style.name)){
        style.name <- 'default'
        message('style.name not specified, so using "default" style.')
    }
    
    cyrestGET(paste('styles',style.name,'mappings', sep = '/'), 
              base.url=base.url)
}


# ==============================================================================
# II. Specific Functions
# ==============================================================================
# II.a. Node Properties
# Pattern: (1) prepare mapVisualProperty, (2) call updateStyleMapping()
# ------------------------------------------------------------------------------
#' @title Set Node Border Color Mapping
#'
#' @description Map table column values to colors to set the node border color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See 
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is 
#' http://localhost:1234 and the latest version of the CyREST API supported by 
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeBorderColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setNodeBorderColorMapping('score', colors=paletteColorBrewerRdBu)
#' setNodeBorderColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setNodeBorderColorMapping <- function (table.column, table.column.values=NULL, colors=NULL, 
                                       mapping.type='c', default.color=NULL, style.name=NULL, 
                                       network=NULL, base.url=.defaultBaseUrl) {
    # check for color palette use case
    if(typeof(colors) == "closure"){ #i.e., name of palette function
        if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
            auto.map<-.genColorMap('node',table.column,colors,mapping.type,
                              network,base.url)
            table.column.values<-auto.map$table.column.values
            colors<-auto.map$colors
        } else {
            colors <- colors(length(table.column.values))
        }
    }
    
    # check if colors are formatted correctly
    colors.checked = NULL
    for (color in colors) {
        colors.checked <- c(colors.checked, .checkHexColor(color))
    }
    
    # set default color
    if(!is.null(default.color))
        setNodeBorderColorDefault(default.color, style.name, base.url=base.url)
    
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("NODE_BORDER_PAINT",table.column, 'c',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("NODE_BORDER_PAINT",table.column, 'd',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("NODE_BORDER_PAINT",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
} 

# ------------------------------------------------------------------------------
#' @title Set Node Border Opacity Mapping
#'
#' @description Sets opacity for node border only.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in 
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped 
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeBorderOpacityMapping('score')
#' setNodeBorderOpacityMapping('score', opacities=c(0,100))
#' setNodeBorderOpacityMapping('score', c(-5,5), c(50,255))
#' }
#' @export
setNodeBorderOpacityMapping <- function(table.column, table.column.values=NULL, 
                                        opacities=NULL, mapping.type='c', 
                                        default.opacity=NULL, style.name=NULL, 
                                        network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column,'node',network, base.url)) 
        stop("Table column does not exist. Please try again.")
    for (o in opacities){
        .checkOpacity(o)
    }
    if(!is.null(default.opacity)){
        .checkOpacity(default.opacity)
        setVisualPropertyDefault(
            list(visualProperty = "NODE_BORDER_TRANSPARENCY", value = default.opacity), 
            style.name, base.url)
    }
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genOpacityMap('node',table.column,opacities,mapping.type,
                            network,base.url)
        table.column.values<-auto.map$table.column.values
        opacities<-auto.map$opacities
    }
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp1 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'c',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp1 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'd',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp1 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'p',
                                  network=network, base.url = base.url)
    } else {
        stop("Mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp1, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Border Width Mapping
#'
#' @description Map table column values to widths to set the node border width.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param widths List of width values to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.width Width value to set as default for all unmapped values 
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeBorderWidthMapping('score')
#' setNodeBorderWidthMapping('score', widths=c(1,10))
#' setNodeBorderWidthMapping('score', c(0,30), c(1,5))
#' }
#' @export
setNodeBorderWidthMapping <- function (table.column, table.column.values=NULL, widths=NULL, 
                                       mapping.type='c', default.width=NULL, style.name=NULL, 
                                       network=NULL, base.url=.defaultBaseUrl) {
    # set default
    if(!is.null(default.width))
        setNodeBorderWidthDefault(default.width, style.name, base.url=base.url)
    
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genDimMap('node',table.column,widths,mapping.type,
                            network,base.url)
        table.column.values<-auto.map$table.column.values
        widths<-auto.map$dims
    }
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("NODE_BORDER_WIDTH",table.column, 'c',
                                 table.column.values, widths, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("NODE_BORDER_WIDTH",table.column, 'd',
                                 table.column.values, widths, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("NODE_BORDER_WIDTH",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Color Mapping
#'
#' @description Map table column values to colors to set the node fill color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See 
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is 
#' http://localhost:1234 and the latest version of the CyREST API supported by 
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeColorMapping('score', c(-5,0,5), c('#5577FF','#FFFFFF','#FF7755'))
#' setNodeColorMapping('score', colors=paletteColorBrewerRdBu)
#' setNodeColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setNodeColorMapping <- function (table.column, table.column.values=NULL, colors=NULL, 
                                 mapping.type='c', default.color=NULL, style.name=NULL, 
                                 network=NULL, base.url=.defaultBaseUrl) {
    # check for color palette use case
    if(typeof(colors) == "closure"){ #i.e., name of palette function
        if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
            auto.map<-.genColorMap('node',table.column,colors,mapping.type,
                              network,base.url)
            table.column.values<-auto.map$table.column.values
            colors<-auto.map$colors
        } else {
                colors <- colors(length(table.column.values))
        }
    }
    
    # check if colors are formatted correctly
    colors.checked = NULL
    for (color in colors) {
        colors.checked <- c(colors.checked, .checkHexColor(color))
    }
    
    # set default
    if(!is.null(default.color))
        setNodeColorDefault(default.color, style.name, base.url=base.url)
    
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("NODE_FILL_COLOR",table.column, 'c',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("NODE_FILL_COLOR",table.column, 'd',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("NODE_FILL_COLOR",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
} 

# ------------------------------------------------------------------------------
#' @title Set Node Combo Opacity Mapping
#'
#' @description Sets opacity for node fill, border and label all together.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in 
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped 
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeComboOpacityMapping('score')
#' setNodeComboOpacityMapping('score', opacities=c(0,100))
#' setNodeComboOpacityMapping('score', c(-5,5), c(50,255))
#' }
#' @export
setNodeComboOpacityMapping <- function (table.column, table.column.values=NULL, 
                                        opacities=NULL, mapping.type='c',
                                        default.opacity=NULL, style.name=NULL, 
                                        network=NULL, base.url=.defaultBaseUrl) {
    
    # check if opacities are formatted correctly
    for (o in opacities){
        .checkOpacity(o)
    }
    
    # set default
    if(!is.null(default.opacity)){
        .checkOpacity(default.opacity)
        setVisualPropertyDefault(
            list(visualProperty = "NODE_TRANSPARENCY", value = default.opacity), 
            style.name, base.url)
        setVisualPropertyDefault(
            list(visualProperty = "NODE_BORDER_TRANSPARENCY", value = default.opacity), 
            style.name, base.url)
        setVisualPropertyDefault(
            list(visualProperty = "NODE_LABEL_TRANSPARENCY", value = default.opacity), 
            style.name, base.url)
    }
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genOpacityMap('node',table.column,opacities,mapping.type,
                            network,base.url)
        table.column.values<-auto.map$table.column.values
        opacities<-auto.map$opacities
    }
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'c',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
        mvp2 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'c',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
        mvp3 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'c',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'd',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
        mvp2 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'd',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
        mvp3 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'd',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'p',
                                  network=network, base.url = base.url)
        mvp2 <- mapVisualProperty("NODE_BORDER_TRANSPARENCY",table.column, 'p',
                                  network=network, base.url = base.url)
        mvp3 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'p',
                                  network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp1, base.url = base.url)
    updateStyleMapping(style.name, mvp2, base.url = base.url)
    updateStyleMapping(style.name, mvp3, base.url = base.url)
} 

# ------------------------------------------------------------------------------
#' @title Set Node Fill Opacity Mapping
#'
#' @description Sets opacity for node fill only.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in 
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped 
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeFillOpacityMapping('score')
#' setNodeFillOpacityMapping('score', opacities=c(0,100))
#' setNodeFillOpacityMapping('score', c(-5,5), c(50,255))
#' }
#' @export
setNodeFillOpacityMapping <- function(table.column, table.column.values=NULL, 
                                        opacities=NULL, mapping.type='c', 
                                        default.opacity=NULL, style.name=NULL, 
                                        network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column,'node',network, base.url)) 
        stop("Table column does not exist. Please try again.")
    for (o in opacities){
        .checkOpacity(o)
    }
    if(!is.null(default.opacity)){
        .checkOpacity(default.opacity) 
        setVisualPropertyDefault(
            list(visualProperty = "NODE_TRANSPARENCY", value = default.opacity), 
            style.name, base.url)
    }
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genOpacityMap('node',table.column,opacities,mapping.type,
                            network,base.url)
        table.column.values<-auto.map$table.column.values
        opacities<-auto.map$opacities
    }
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'c',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'd',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp1 <- mapVisualProperty("NODE_TRANSPARENCY",table.column, 'p',
                                  network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp1, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Node Font Face Mapping
#'
#' @description Sets font face for node labels.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in 
#' mapping
#' @param fonts List of string specifications of font face, style and size, e.g., 
#' c("SansSerif,plain,12", "Dialog,plain,10")
#' @param mapping.type (char) discrete or passthrough (d,p); 
#' default is discrete
#' @param default.font String specification of font face, style and size, e.g., 
#' "SansSerif,plain,12" or "Dialog,plain,10"
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeFontFaceMapping("myfonts", c("normal","small"),
#' c("SansSerif,plain,12", "Dialog,plain,10"))
#' }
#' @export
setNodeFontFaceMapping <- function(table.column, table.column.values, 
                                   fonts, mapping.type='d', 
                                   default.font=NULL,
                                   style.name=NULL, 
                                   network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column,'node',network, base.url)) 
        stop("Table column does not exist. Please try again.")
    if(!is.null(default.font)){
        setVisualPropertyDefault(
            list(visualProperty = "NODE_LABEL_FONT_FACE", value = default.font), 
            style.name, base.url)
    }
    if (mapping.type %in% c('continuous','c','interpolate')) {
        stop("Continuous mapping of font face values is not supported.")
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp1 <- mapVisualProperty("NODE_LABEL_FONT_FACE",table.column, 'd',
                                  table.column.values, fonts, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp1 <- mapVisualProperty("NODE_LABEL_FONT_FACE",table.column, 'p',
                                  network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp1, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Node Font Size Mapping
#'
#' @description Map table column values to sizes to set the node size.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param sizes List of sizes to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.size Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeFontSizeMapping('score')
#' setNodeFontSizeMapping('score', sizes=c(6,24))
#' setNodeFontSizeMapping('score', c(0,30), c(35,55))
#' }
#' @export
setNodeFontSizeMapping <- function (table.column, table.column.values=NULL, sizes=NULL, 
                                mapping.type='c', default.size=NULL, style.name=NULL, 
                                network=NULL, base.url=.defaultBaseUrl) {
    # set default
    if(!is.null(default.size))
        setNodeFontSizeDefault(default.size, style.name, base.url=base.url)
    
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genDimMap('node',table.column,sizes,mapping.type,
                             network,base.url)
        table.column.values<-auto.map$table.column.values
        sizes<-auto.map$dims
    }
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("NODE_LABEL_FONT_SIZE",table.column, 'c',
                                 table.column.values, sizes, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("NODE_LABEL_FONT_SIZE",table.column, 'd',
                                 table.column.values, sizes, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("NODE_LABEL_FONT_SIZE",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Node Height Mapping
#'
#' @description Map table column values to the node heights.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param heights List of height values to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.height Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @details Using this function will unlock node width and height to use  
#' separate values.
#' @examples \donttest{
#' setNodeHeightMapping('score')
#' setNodeHeightMapping('score', heights=c(30,80))
#' setNodeHeightMapping('score', c(0,30), c(35,55))
#' }
#' @export
setNodeHeightMapping <- function (table.column, table.column.values=NULL, heights=NULL, 
                                mapping.type='c', default.height=NULL, style.name=NULL, 
                                network=NULL, base.url=.defaultBaseUrl) {
    lockNodeDimensions(FALSE, style.name,base.url)
    
    # set default
    if(!is.null(default.height))
        setNodeHeightDefault(default.height, style.name, base.url=base.url)
    
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genDimMap('node',table.column,heights,mapping.type,
                             network,base.url)
        table.column.values<-auto.map$table.column.values
        heights<-auto.map$dims
    }
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("NODE_HEIGHT",table.column, 'c',
                                 table.column.values, heights, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("NODE_HEIGHT",table.column, 'd',
                                 table.column.values, heights, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("NODE_HEIGHT",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Node Label Mapping
#'
#' @description Pass the values from a table column to display as node labels.
#' @param table.column Name of Cytoscape table column to map values from
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeLabelMapping('name')
#' }
#' @export
setNodeLabelMapping <- function (table.column, style.name=NULL, 
                                 network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column,'node',network, base.url)) return()
    mvp <- mapVisualProperty("NODE_LABEL", table.column, 'p', 
                             network = network, base.url = base.url)  
    updateStyleMapping(style.name, mvp, base.url = base.url)
}


# ------------------------------------------------------------------------------
#' @title Set Node Label Color Mapping
#'
#' @description Map table column values to colors to set the node border color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See 
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is 
#' http://localhost:1234 and the latest version of the CyREST API supported by 
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeLabelColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setNodeLabelColorMapping('score', colors=paletteColorBrewerRdBu)
#' setNodeLabelColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setNodeLabelColorMapping <- function (table.column, table.column.values=NULL, colors=NULL, 
                                       mapping.type='c', default.color=NULL, style.name=NULL, 
                                       network=NULL, base.url=.defaultBaseUrl) {
    # check for color palette use case
    if(typeof(colors) == "closure"){ #i.e., name of palette function
        if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
            auto.map<-.genColorMap('node',table.column,colors,mapping.type,
                              network,base.url)
            table.column.values<-auto.map$table.column.values
            colors<-auto.map$colors
        } else {
            colors <- colors(length(table.column.values))
        }
    }
    
    # check if colors are formatted correctly
    colors.checked = NULL
    for (color in colors) {
        colors.checked <- c(colors.checked, .checkHexColor(color))
    }
    
    # set default
    if(!is.null(default.color))
        setNodeLabelColorDefault(default.color, style.name, base.url=base.url)
    
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("NODE_LABEL_COLOR",table.column, 'c',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("NODE_LABEL_COLOR",table.column, 'd',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("NODE_LABEL_COLOR",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Node Label Opacity Mapping
#'
#' @description Sets opacity for node label only.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in 
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped 
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeLabelOpacityMapping('score')
#' setNodeLabelOpacityMapping('score', opacities=c(0,100))
#' setNodeLabelOpacityMapping('score', c(-5,5), c(50,255))
#' }
#' @export
setNodeLabelOpacityMapping <- function(table.column, table.column.values=NULL, 
                                        opacities=NULL, mapping.type='c', 
                                        default.opacity=NULL, style.name=NULL, 
                                        network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column,'node',network, base.url)) 
        stop("Table column does not exist. Please try again.")
    for (o in opacities){
        .checkOpacity(o)
    }
    if(!is.null(default.opacity)){
        .checkOpacity(default.opacity)
        setVisualPropertyDefault(
            list(visualProperty = "NODE_LABEL_TRANSPARENCY", value = default.opacity), 
            style.name, base.url)
    }
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genOpacityMap('node',table.column,opacities,mapping.type,
                            network,base.url)
        table.column.values<-auto.map$table.column.values
        opacities<-auto.map$opacities
    }
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp1 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'c',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp1 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'd',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp1 <- mapVisualProperty("NODE_LABEL_TRANSPARENCY",table.column, 'p',
                                  network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp1, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Node Shape Mapping
#'
#' @description Map table column values to shapes to set the node shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to 
#' perform an automatic mapping to available shapes. See \link{getNodeShapes}
#' @param default.shape Shape to set as default. See \link{getNodeShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeShapeMapping('type')
#' setNodeShapeMapping('type',c('protein','dna'),c('ELLIPSE','RECTANGLE'))
#' }
#' @export
setNodeShapeMapping <- function (table.column, table.column.values=NULL, 
                                 shapes=NULL, 
                                 default.shape=NULL , style.name=NULL, 
                                 network=NULL, base.url=.defaultBaseUrl) {
    # set default
    if(!is.null(default.shape))
        setNodeShapeDefault(default.shape, style.name, base.url=base.url)
    # check table.column.values to map
    if(is.null(table.column.values)){
        auto.map<-.genShapeMap(table.column,
                               network,base.url)
        table.column.values<-auto.map$table.column.values
        shapes<-auto.map$shapes
    }
    # perform mapping
    mvp <- mapVisualProperty("NODE_SHAPE",table.column, 'd',
                             table.column.values, shapes, 
                             network=network, base.url = base.url)
    
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Node Size Mapping
#'
#' @description Map table column values to node font sizes.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param sizes List of sizes to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.size Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @details Using this function will lock node width and height to use a 
#' singular "size" value.
#' @examples \donttest{
#' setNodeSizeMapping('score')
#' setNodeSizeMapping('score', sizes=c(30,80))
#' setNodeSizeMapping('score', c(0,30), c(35,55))
#' }
#' @export
setNodeSizeMapping <- function (table.column, table.column.values=NULL, sizes=NULL, 
                                mapping.type='c', default.size=NULL, style.name=NULL, 
                                network=NULL, base.url=.defaultBaseUrl) {
    
    lockNodeDimensions(TRUE,style.name, base.url)
    
    # set default
    if(!is.null(default.size))
        setNodeSizeDefault(default.size, style.name, base.url=base.url)
    
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genDimMap('node',table.column,sizes,mapping.type,
                             network,base.url)
        table.column.values<-auto.map$table.column.values
        sizes<-auto.map$dims
    }
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("NODE_SIZE",table.column, 'c',
                                 table.column.values, sizes, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("NODE_SIZE",table.column, 'd',
                                 table.column.values, sizes, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("NODE_SIZE",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Node Tooltip Mapping
#'
#' @description Pass the values from a table column to display as node tooltips.
#' @param table.column Name of Cytoscape table column to map values from
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setNodeTooltipMapping('description')
#' }
#' @export
setNodeTooltipMapping <- function (table.column, style.name=NULL, 
                                   network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column,'node',network, base.url)) return()
    mvp <- mapVisualProperty("NODE_TOOLTIP", table.column, 'p', 
                             network = network, base.url = base.url)  
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Node Width Mapping
#'
#' @description Map table column values to the node widths.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param widths List of width values to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.width Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. 
#' Default is the "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' #' @details Using this function will unlock node width and height to use  
#' separate values.
#' @examples \donttest{
#' setNodeWidthMapping('score')
#' setNodeWidthMapping('score', widths=c(30,80))
#' setNodeWidthMapping('score', c(0,30), c(35,55))
#' }
#' @export
setNodeWidthMapping <- function (table.column, table.column.values=NULL, widths=NULL, 
                                  mapping.type='c', default.width=NULL, style.name=NULL, 
                                  network=NULL, base.url=.defaultBaseUrl) {
    lockNodeDimensions(FALSE, style.name, base.url)
    
    # set default
    if(!is.null(default.width))
        setNodeWidthDefault(default.width, style.name, base.url=base.url)
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genDimMap('node',table.column,widths,mapping.type,
                             network,base.url)
        table.column.values<-auto.map$table.column.values
        widths<-auto.map$dims
    }
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("NODE_WIDTH",table.column, 'c',
                                 table.column.values, widths, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("NODE_WIDTH",table.column, 'd',
                                 table.column.values, widths, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("NODE_WIDTH",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ==============================================================================
# II.b. Edge Properties
# Pattern: (1) prepare mapVisualProperty, (2) call updateStyleMapping()
# ------------------------------------------------------------------------------
#' @title Set Edge Color Mapping
#'
#' @description Map table column values to colors to set the edge color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See 
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is 
#' http://localhost:1234 and the latest version of the CyREST API supported by 
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setEdgeColorMapping('score', colors=paletteColorBrewerRdBu)
#' setEdgeColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setEdgeColorMapping <- function (table.column, table.column.values=NULL, colors=NULL, 
                                 mapping.type='c', default.color=NULL, style.name=NULL, 
                                 network=NULL, base.url=.defaultBaseUrl) {
    # check for color palette use case
    if(typeof(colors) == "closure"){ #i.e., name of palette function
        if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
            auto.map<-.genColorMap('edge',table.column,colors,mapping.type,
                              network,base.url)
            table.column.values<-auto.map$table.column.values
            colors<-auto.map$colors
        } else {
            colors <- colors(length(table.column.values))
        }
    }
    
    # check if colors are formatted correctly
    colors.checked = NULL
    for (color in colors) {
        colors.checked <- c(colors.checked, .checkHexColor(color))
    }
    
    # set default
    if(!is.null(default.color))
        setEdgeColorDefault(default.color, style.name, base.url=base.url)
    
    # perform mapping for COLOR (i.e., when arrowColorMatchesEdge=T)
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("EDGE_UNSELECTED_PAINT",table.column, 'c',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("EDGE_UNSELECTED_PAINT",table.column, 'd',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("EDGE_UNSELECTED_PAINT",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
    
    # perform mapping for STROKE (i.e., when arrowColorMatchesEdge=F)
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("EDGE_STROKE_UNSELECTED_PAINT",table.column, 'c',
                                 table.column.values, colors, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("EDGE_STROKE_UNSELECTED_PAINT",table.column, 'd',
                                 table.column.values, colors, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("EDGE_STROKE_UNSELECTED_PAINT",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
    
} 

# ------------------------------------------------------------------------------
#' @title Set Edge Font Face Mapping
#'
#' @description Sets font face for edge labels.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in 
#' mapping
#' @param fonts List of string specifications of font face, style and size, e.g., 
#' c("SansSerif,plain,12", "Dialog,plain,10")
#' @param mapping.type (char) discrete or passthrough (d,p); 
#' default is discrete
#' @param default.font String specification of font face, style and size, e.g., 
#' "SansSerif,plain,12" or "Dialog,plain,10"
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeFontFaceMapping("myfonts", c("normal","small"),
#' c("SansSerif,plain,12", "Dialog,plain,10"))
#' }
#' @export
setEdgeFontFaceMapping <- function(table.column, table.column.values, 
                                   fonts, mapping.type='d', 
                                   default.font=NULL,
                                   style.name=NULL, 
                                   network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column,'edge',network, base.url)) 
        stop("Table column does not exist. Please try again.")
    if(!is.null(default.font)){
        setVisualPropertyDefault(
            list(visualProperty = "EDGE_LABEL_FONT_FACE", value = default.font), 
            style.name, base.url)
    }
    if (mapping.type %in% c('continuous','c','interpolate')) {
        stop("Continuous mapping of font face values is not supported.")
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp1 <- mapVisualProperty("EDGE_LABEL_FONT_FACE",table.column, 'd',
                                  table.column.values, fonts, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp1 <- mapVisualProperty("EDGE_LABEL_FONT_FACE",table.column, 'p',
                                  network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp1, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Edge Font Size Mapping
#'
#' @description Map table column values to sizes to set the edge size.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param sizes List of sizes to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.size Size value to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeFontSizeMapping('score')
#' setEdgeFontSizeMapping('score', sizes=c(6,24))
#' setEdgeFontSizeMapping('score', c(0,30), c(35,55))
#' }
#' @export
setEdgeFontSizeMapping <- function (table.column, table.column.values=NULL, sizes=NULL, 
                                    mapping.type='c', default.size=NULL, style.name=NULL, 
                                    network=NULL, base.url=.defaultBaseUrl) {
    # set default
    if(!is.null(default.size))
        setEdgeFontSizeDefault(default.size, style.name, base.url=base.url)
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genDimMap('edge',table.column,sizes,mapping.type,
                             network,base.url)
        table.column.values<-auto.map$table.column.values
        sizes<-auto.map$dims
    }
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("EDGE_LABEL_FONT_SIZE",table.column, 'c',
                                 table.column.values, sizes, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("EDGE_LABEL_FONT_SIZE",table.column, 'd',
                                 table.column.values, sizes, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("EDGE_LABEL_FONT_SIZE",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Label Mapping
#'
#' @description Pass the values from a table column to display as edge labels.
#' @param table.column Name of Cytoscape table column to map values from
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLabelMapping('label')
#' }
#' @export
setEdgeLabelMapping <- function (table.column, style.name=NULL, 
                                 network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column, 'edge',network, base.url)) return()
    mvp <- mapVisualProperty("EDGE_LABEL", table.column, 'p')  
    updateStyleMapping(style.name, mvp, base.url = base.url)
}
#' @export
# ------------------------------------------------------------------------------
#' @title Set Edge Label Color Mapping
#'
#' @description Map table column values to colors to set the edge border color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See 
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is 
#' http://localhost:1234 and the latest version of the CyREST API supported by 
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLabelColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setEdgeLabelColorMapping('score', colors=paletteColorBrewerRdBu)
#' setEdgeLabelColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setEdgeLabelColorMapping <- function (table.column, table.column.values=NULL, colors=NULL, 
                                      mapping.type='c', default.color=NULL, style.name=NULL, 
                                      network=NULL, base.url=.defaultBaseUrl) {
    # check for color palette use case
    if(typeof(colors) == "closure"){ #i.e., name of palette function
        if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
            auto.map<-.genColorMap('edge',table.column,colors,mapping.type,
                              network,base.url)
            table.column.values<-auto.map$table.column.values
            colors<-auto.map$colors
        } else {
            colors <- colors(length(table.column.values))
        }
    }
    
    # check if colors are formatted correctly
    colors.checked = NULL
    for (color in colors) {
        colors.checked <- c(colors.checked, .checkHexColor(color))
    }
    
    # set default
    if(!is.null(default.color))
        setEdgeLabelColorDefault(default.color, style.name, base.url=base.url)
    
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("EDGE_LABEL_COLOR",table.column, 'c',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("EDGE_LABEL_COLOR",table.column, 'd',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("EDGE_LABEL_COLOR",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Edge Label Opacity Mapping
#'
#' @description Sets opacity for edge label only.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in 
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped 
#' values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLabelOpacityMapping('weight')
#' setEdgeLabelOpacityMapping('weight', opacities=c(0,100))
#' setEdgeLabelOpacityMapping('weight', c(1,10), c(50,255))
#' }
#' @export
setEdgeLabelOpacityMapping <- function(table.column, table.column.values=NULL, 
                                   opacities=NULL, mapping.type='c', 
                                   default.opacity=NULL,
                                   style.name=NULL, 
                                   network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column,'edge',network, base.url)) 
        stop("Table column does not exist. Please try again.")
    for (o in opacities){
        .checkOpacity(o)
    }
    if(!is.null(default.opacity)){
        .checkOpacity(default.opacity)
        setVisualPropertyDefault(
            list(visualProperty = "EDGE_LABEL_TRANSPARENCY", value = default.opacity), 
            style.name, base.url)
    }
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genOpacityMap('edge',table.column,opacities,mapping.type,
                            network,base.url)
        table.column.values<-auto.map$table.column.values
        opacities<-auto.map$opacities
    }
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp1 <- mapVisualProperty("EDGE_LABEL_TRANSPARENCY",table.column, 'c',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp1 <- mapVisualProperty("EDGE_LABEL_TRANSPARENCY",table.column, 'd',
                                  table.column.values, opacities, 
                                  network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp1 <- mapVisualProperty("EDGE_LABEL_TRANSPARENCY",table.column, 'p',
                                  network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp1, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Line Style Mapping
#'
#' @description Map table column values to styles to set the edge style.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param line.styles List of line styles. Leave NULL to perform
#' an automatic mapping to available line styles. See \link{getLineStyles}.
#' @param default.line.style Style to set as default. See \link{getLineStyles}.
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLineStyleMapping('type')
#' setEdgeLineStyleMapping('type',c('pp','pd'),c('SOLID','LONG_DASH'))
#' }
#' @export
setEdgeLineStyleMapping <- function (table.column, table.column.values=NULL, 
                                     line.styles=NULL, 
                                     default.line.style='SOLID', style.name=NULL, 
                                     network=NULL, base.url=.defaultBaseUrl) {
    # set default
    if(!is.null(default.line.style))
        setEdgeLineStyleDefault(default.line.style, style.name, base.url=base.url)
    # check table.column.values to map
    if(is.null(table.column.values)){
        auto.map<-.genLineStyleMap(table.column,
                                 network,base.url)
        table.column.values<-auto.map$table.column.values
        line.styles<-auto.map$line.styles
    }
    # perform mapping
    mvp <- mapVisualProperty("EDGE_LINE_TYPE",table.column, 'd',
                             table.column.values, line.styles, 
                             network=network, base.url = base.url)
    
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Edge Line Width Mapping
#'
#' @description Map table column values to widths to set the edge line width.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param widths List of width values to map to table.column.values. A range
#' of 10 to 100 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.width Width value to set as default for all unmapped values for all unmapped values.
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeLineWidthMapping('score')
#' setEdgeLineWidthMapping('score', widths=c(1,10))
#' setEdgeLineWidthMapping('score', c(0,30), c(1,5))
#' }
#' @export
setEdgeLineWidthMapping <- function (table.column, table.column.values=NULL, widths=NULL, 
                                     mapping.type='c', default.width=NULL, style.name=NULL, 
                                     network=NULL, base.url=.defaultBaseUrl) {
    # set default
    if(!is.null(default.width))
        setEdgeLineWidthDefault(default.width, style.name, base.url=base.url)
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genDimMap('edge',table.column,widths,mapping.type,
                             network,base.url)
        table.column.values<-auto.map$table.column.values
        widths<-auto.map$dims
    }
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("EDGE_WIDTH",table.column, 'c',
                                 table.column.values, widths, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("EDGE_WIDTH",table.column, 'd',
                                 table.column.values, widths, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("EDGE_WIDTH",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Edge Opacity Mapping
#'
#' @description Map table column values to opacities to set the edge opacity.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param opacities (integer) values between 0 and 255; 0 is invisible. A range
#' of 50 to 255 is used by default for automatic mapping.
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); default is continuous
#' @param default.opacity Opacity value to set as default for all unmapped values
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeOpacityMapping('weight')
#' setEdgeOpacityMapping('weight', opacities=c(0,100))
#' setEdgeOpacityMapping('weight', c(1,10), c(50,255))
#' }
#' @export
setEdgeOpacityMapping <- function (table.column, table.column.values=NULL, 
                                   opacities=NULL, mapping.type='c',
                                   default.opacity=NULL, style.name=NULL, 
                                   network=NULL, base.url=.defaultBaseUrl) {
    
    # check if opacities are formatted correctly
    for (o in opacities){
        .checkOpacity(o)
    }
    
    # set default
    if(!is.null(default.opacity)){
        .checkOpacity(default.opacity)
        setVisualPropertyDefault(
            list(visualProperty = "EDGE_TRANSPARENCY", value = default.opacity), 
            style.name, base.url)
    }   
    # check table.column.values to map
    if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
        auto.map<-.genOpacityMap('edge',table.column,opacities,mapping.type,
                            network,base.url)
        table.column.values<-auto.map$table.column.values
        opacities<-auto.map$opacities
    }
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("EDGE_TRANSPARENCY",table.column, 'c',
                                 table.column.values, opacities, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("EDGE_TRANSPARENCY",table.column, 'd',
                                 table.column.values, opacities, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("EDGE_TRANSPARENCY",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
} 
# ------------------------------------------------------------------------------
#' @title Set Edge Target Arrow Mapping
#'
#' @description Map table column values to shapes to set the target arrow shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to 
#' perform an automatic mapping to available shapes. See \link{getArrowShapes}
#' @param default.shape Shape to set as default. See \link{getArrowShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeTargetArrowMapping('type')
#' setEdgeTargetArrowMapping('type',c('activation','inhibition'),c('ARROW','T'))
#' }
#' @export
setEdgeTargetArrowMapping <- function (table.column, table.column.values=NULL, 
                                       shapes=NULL, 
                                       default.shape='ARROW', style.name=NULL, 
                                       network=NULL, base.url=.defaultBaseUrl) {
    #Whoops! Duplicate?? TODO: Deprecate?
    setEdgeTargetArrowShapeMapping(table.column, table.column.values, shapes, 
                                   default.shape , style.name, 
                                   network, base.url) 
}

# ------------------------------------------------------------------------------
#' @title Set Edge Source Arrow Mapping
#'
#' @description Map table column values to shapes to set the source arrow shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to 
#' perform an automatic mapping to available shapes. See \link{getArrowShapes}
#' @param default.shape Shape to set as default. See \link{getArrowShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeSourceArrowMapping('type')
#' setEdgeSourceArrowMapping('type',c('activation','inhibition'),c('ARROW','T'))
#' }
#' @export
setEdgeSourceArrowMapping <- function (table.column, table.column.values=NULL, 
                                       shapes=NULL, 
                                       default.shape='ARROW', style.name=NULL, 
                                       network=NULL, base.url=.defaultBaseUrl) {
    #Whoops! Duplicate?? TODO: Deprecate?
    setEdgeSourceArrowShapeMapping(table.column, table.column.values, shapes, 
                                   default.shape , style.name, 
                                   network, base.url) 
}


# ------------------------------------------------------------------------------
#' @title Set Edge Target Arrow Color Mapping
#'
#' @description Map table column values to colors to set the target arrow color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See 
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is 
#' http://localhost:1234 and the latest version of the CyREST API supported by 
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeTargetArrowColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setEdgeTargetArrowColorMapping('score', colors=paletteColorBrewerRdBu)
#' setEdgeTargetArrowColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setEdgeTargetArrowColorMapping <- function (table.column, table.column.values=NULL, colors=NULL, 
                                            mapping.type='c', default.color=NULL, style.name=NULL, 
                                            network=NULL, base.url=.defaultBaseUrl) {
    # check for color palette use case
    if(typeof(colors) == "closure"){ #i.e., name of palette function
        if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
            auto.map<-.genColorMap('edge',table.column,colors,mapping.type,
                              network,base.url)
            table.column.values<-auto.map$table.column.values
            colors<-auto.map$colors
        } else {
            colors <- colors(length(table.column.values))
        }
    }
    # check if colors are formatted correctly
    colors.checked = NULL
    for (color in colors) {
        colors.checked <- c(colors.checked, .checkHexColor(color))
    }
    
    # set default
    if(!is.null(default.color))
        setEdgeTargetArrowColorDefault(default.color, style.name, base.url=base.url)
    
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("EDGE_TARGET_ARROW_UNSELECTED_PAINT",table.column, 'c',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("EDGE_TARGET_ARROW_UNSELECTED_PAINT",table.column, 'd',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("EDGE_TARGET_ARROW_UNSELECTED_PAINT",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
} 

# ------------------------------------------------------------------------------
#' @title Set Edge Source Arrow Color Mapping
#'
#' @description Map table column values to colors to set the source arrow color.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used in
#' mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param colors List of hex colors to map to table.column.values or a color
#' palette function, e.g., paletteColorBrewerSet3 (without quotes). See 
#' RColorBrewer::display.brewer.all()
#' @param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#' default is continuous
#' @param default.color Hex color to set as default
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the 
#' "current" network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is 
#' http://localhost:1234 and the latest version of the CyREST API supported by 
#' this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeSourceArrowColorMapping('score', c(0,5), c('#FFFFFF','#FF7755'))
#' setEdgeSourceArrowColorMapping('score', colors=paletteColorBrewerRdBu)
#' setEdgeSourceArrowColorMapping('score', colors=paletteColorBrewerSet3, mapping.type='d')
#' }
#' @export
setEdgeSourceArrowColorMapping <- function (table.column, table.column.values=NULL, colors=NULL, 
                                            mapping.type='c', default.color=NULL, style.name=NULL, 
                                            network=NULL, base.url=.defaultBaseUrl) {
    # check for color palette use case
    if(typeof(colors) == "closure"){ #i.e., name of palette function
        if(is.null(table.column.values) && mapping.type %in% c('continuous','c','interpolate')){
            auto.map<-.genColorMap('edge',table.column,colors,mapping.type,
                              network,base.url)
            table.column.values<-auto.map$table.column.values
            colors<-auto.map$colors
        } else {
            colors <- colors(length(table.column.values))
        }
    }
    # check if colors are formatted correctly
    colors.checked = NULL
    for (color in colors) {
        colors.checked <- c(colors.checked, .checkHexColor(color))
    }
    
    # set default
    if(!is.null(default.color))
        setEdgeSourceArrowColorDefault(default.color, style.name, base.url=base.url)
    
    # perform mapping
    if (mapping.type %in% c('continuous','c','interpolate')) {
        mvp <- mapVisualProperty("EDGE_SOURCE_ARROW_UNSELECTED_PAINT",table.column, 'c',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('discrete','d','lookup')){
        mvp <- mapVisualProperty("EDGE_SOURCE_ARROW_UNSELECTED_PAINT",table.column, 'd',
                                 table.column.values, colors.checked, 
                                 network=network, base.url = base.url)
    } else if (mapping.type %in% c('passthrough','p')){
        mvp <- mapVisualProperty("EDGE_SOURCE_ARROW_UNSELECTED_PAINT",table.column, 'p',
                                 network=network, base.url = base.url)
    } else {
        stop("mapping.type not recognized.")
        
    }
    updateStyleMapping(style.name, mvp, base.url = base.url)
} 

# ------------------------------------------------------------------------------
#' @title Set Edge Target Arrow Shape Mapping
#'
#' @description Map table column values to shapes to set the target arrow shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to 
#' perform an automatic mapping to available shapes. See \link{getArrowShapes}
#' @param default.shape Shape to set as default. See \link{getArrowShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeTargetArrowShapeMapping('type')
#' setEdgeTargetArrowShapeMapping('type',c('activation','inhibition'),
#'   c('ARROW','T'))
#' }
#' @export
setEdgeTargetArrowShapeMapping <- function(table.column, 
                          table.column.values=NULL, shapes=NULL, 
                          default.shape=NULL , style.name=NULL, 
                          network=NULL, base.url=.defaultBaseUrl) {
    # set default
    if(!is.null(default.shape))
        setEdgeTargetArrowShapeDefault(default.shape, style.name, base.url=base.url)
    # check table.column.values to map
    if(is.null(table.column.values)){
        auto.map<-.genArrowMap(table.column,
                                   network,base.url)
        table.column.values<-auto.map$table.column.values
        shapes<-auto.map$shapes
    }
    # perform mapping
    mvp <- mapVisualProperty("EDGE_TARGET_ARROW_SHAPE",table.column, 'd',
                             table.column.values, shapes, 
                             network=network, base.url = base.url)
    
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ------------------------------------------------------------------------------
#' @title Set Edge Source Arrow Shape Mapping
#'
#' @description Map table column values to shapes to set the source arrow shape.
#' @param table.column Name of Cytoscape table column to map values from
#' @param table.column.values List of values from Cytoscape table to be used 
#' in mapping. Leave NULL to perform an automatic mapping to all column values.
#' @param shapes List of shapes to map to table.column.values. Leave NULL to 
#' perform an automatic mapping to available shapes. See \link{getArrowShapes}
#' @param default.shape Shape to set as default. See \link{getArrowShapes}
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeSourceArrowShapeMapping('type')
#' setEdgeSourceArrowShapeMapping('type',c('activation','inhibition'),
#'   c('ARROW','T'))
#' }
#' @export
setEdgeSourceArrowShapeMapping <- function(table.column, 
                               table.column.values=NULL, shapes=NULL, 
                               default.shape=NULL , style.name=NULL, 
                               network=NULL, base.url=.defaultBaseUrl) {
    # set default
    if(!is.null(default.shape))
        setEdgeSourceArrowShapeDefault(default.shape, style.name, base.url=base.url)
    # check table.column.values to map
    if(is.null(table.column.values)){
        auto.map<-.genArrowMap(table.column,
                                   network,base.url)
        table.column.values<-auto.map$table.column.values
        shapes<-auto.map$shapes
    }
    # perform mapping
    mvp <- mapVisualProperty("EDGE_SOURCE_ARROW_SHAPE",table.column, 'd',
                             table.column.values, shapes, 
                             network=network, base.url = base.url)
    
    updateStyleMapping(style.name, mvp, base.url = base.url)
}
# ------------------------------------------------------------------------------
#' @title Set Edge Tooltip Mapping
#'
#' @description Pass the values from a table column to display as edge tooltips.
#' @param table.column Name of Cytoscape table column to map values from
#' @param style.name Name of style; default is "default" style
#' @param network (optional) Name or SUID of the network. Default is the "current" 
#' network active in Cytoscape.
#' @param base.url (optional) Ignore unless you need to specify a custom domain,
#' port or version to connect to the CyREST API. Default is http://localhost:1234
#' and the latest version of the CyREST API supported by this version of RCy3.
#' @return None
#' @examples \donttest{
#' setEdgeTooltipMapping('description')
#' }
#' @export
setEdgeTooltipMapping <- function (table.column, style.name=NULL, 
                                   network=NULL, base.url=.defaultBaseUrl) {
    if(!.tableColumnExists(table.column, 'edge',network, base.url)) return()
    mvp <- mapVisualProperty("EDGE_TOOLTIP", table.column, 'p')  
    updateStyleMapping(style.name, mvp, base.url = base.url)
}

# ==============================================================================
# III. Palette property value generators
# ------------------------------------------------------------------------------
#'@export
# ------------------------------------------------------------------------------
#' @title paletteColorRandom Qualitative
#'
#' @description Generate a qualitative random color map of a given size
#' @param value.count Number of colors to generate; default is 1
#' @return List of random colors
#' @examples
#' paletteColorRandom()

#' @seealso genNodeColorMap genEdgeColorMap
#' @export
paletteColorRandom<-function(value.count=1){
        if (!requireNamespace("grDevices", quietly = TRUE)) {
            stop("Package \"grDevices\" needed for this function to work. Please install it.",
                call. = FALSE)
        }
        grDevices::rgb(sample(0:255,size=value.count,replace=TRUE), 
        sample(0:255,size=value.count,replace=TRUE), 
        sample(0:255,size=value.count,replace=TRUE), 
        maxColorValue=255)
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPastel2 Qualitative
#'
#' @description Generate a qualitative Pastel2 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 8
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPastel2()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPastel2<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Pastel2'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPastel1 Qualitative
#'
#' @description Generate a qualitative Pastel1 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPastel1()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPastel1<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Pastel1'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerDark2 Qualitative
#'
#' @description Generate a qualitative Dark2 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 8
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerDark2()
 
#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerDark2<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Dark2'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerAccent Qualitative
#'
#' @description Generate a qualitative Accent Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 8
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerAccent()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerAccent<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Accent'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPaired Qualitative
#'
#' @description Generate a qualitative Paired Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 
#' 12. See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPaired()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPaired<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Paired'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerSet1 Qualitative
#'
#' @description Generate a qualitative Set1 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerSet1()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerSet1<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Set1'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerSet2 Qualitative
#'
#' @description Generate a qualitative Set2 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 8
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerSet2()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerSet2<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Set2'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerSet3 Qualitative
#'
#' @description Generate a qualitative Set3 Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 
#' 12. See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerSet3()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerSet3<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Set3'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerYlOrRd Sequential
#'
#' @description Generate a sequential YlOrRd Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerYlOrRd()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerYlOrRd<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'YlOrRd'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerYlOrBr Sequential
#'
#' @description Generate a sequential YlOrBr Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerYlOrBr()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerYlOrBr<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'YlOrBr'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerYlGnBu Sequential
#'
#' @description Generate a sequential YlGnBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerYlGnBu()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerYlGnBu<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'YlGnBu'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerYlGn Sequential
#'
#' @description Generate a sequential YlGn Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerYlGn()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerYlGn<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'YlGn'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerReds Sequential
#'
#' @description Generate a sequential Reds Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerReds()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerReds<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Reds'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerRdPu Sequential
#'
#' @description Generate a sequential RdPu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerRdPu()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerRdPu<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'RdPu'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPurples Sequential
#'
#' @description Generate a sequential Purples Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPurples()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPurples<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Purples'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPuRd Sequential
#'
#' @description Generate a sequential PuRd Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPuRd()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPuRd<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'PuRd'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPuBuGn Sequential
#'
#' @description Generate a sequential PuBuGn Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPuBuGn()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPuBuGn<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'PuBuGn'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPuBu Sequential
#'
#' @description Generate a sequential PuBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPuBu()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPuBu<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'PuBu'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerOrRd Sequential
#'
#' @description Generate a sequential OrRd Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerOrRd()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerOrRd<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'OrRd'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerOranges Sequential
#'
#' @description Generate a sequential Oranges Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerOranges()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerOranges<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Oranges'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerGreys Sequential
#'
#' @description Generate a sequential Greys Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerGreys()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerGreys<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Greys'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerGreens Sequential
#'
#' @description Generate a sequential Greens Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerGreens()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerGreens<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Greens'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerGnBu Sequential
#'
#' @description Generate a sequential GnBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerGnBu()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerGnBu<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'GnBu'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerBuPu Sequential
#'
#' @description Generate a sequential BuPu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerBuPu()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerBuPu<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'BuPu'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerBuGn Sequential
#'
#' @description Generate a sequential BuGn Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples 
#' paletteColorBrewerBuGn()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerBuGn<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'BuGn'))
}

# ------------------------------------------------------------------------------
#' @title paletteColorBrewerBlues Sequential
#'
#' @description Generate a sequential Blues Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerBlues()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerBlues<-function(value.count=3) {
    return(RColorBrewer::brewer.pal(value.count, 'Blues'))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerRdYlBu Divergent
#'
#' @description Generate a divergent RdYlBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerRdYlBu()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerRdYlBu<-function(value.count=3) {
    return(rev(RColorBrewer::brewer.pal(value.count, 'RdYlBu')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerRdBu Divergent
#'
#' @description Generate a divergent RdBu Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerRdBu()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerRdBu<-function(value.count=3) {
    return(rev(RColorBrewer::brewer.pal(value.count, 'RdBu')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPuOr Divergent
#'
#' @description Generate a divergent PuOr Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPuOr()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPuOr<-function(value.count=3) {
    return(rev(RColorBrewer::brewer.pal(value.count, 'PuOr')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPRGn Divergent
#'
#' @description Generate a divergent PRGn Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPRGn()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPRGn<-function(value.count=3) {
    return(rev(RColorBrewer::brewer.pal(value.count, 'PRGn')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerPiYG Divergent
#'
#' @description Generate a divergent PiYG Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerPiYG()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerPiYG<-function(value.count=3) {
    return(rev(RColorBrewer::brewer.pal(value.count, 'PiYG')))
}
# ------------------------------------------------------------------------------
#' @title paletteColorBrewerBrBG Divergent
#'
#' @description Generate a divergent BrBG Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' . See RColorBrewer::display.brewer.all()
#' @return List of palette colors
#' @examples
#' paletteColorBrewerBrBG()

#' @importFrom RColorBrewer brewer.pal
#' @export
paletteColorBrewerBrBG<-function(value.count=3) {
    return(rev(RColorBrewer::brewer.pal(value.count, 'BrBG')))
}

# ------------------------------------------------------------------------------
#' @title paletteColorVirdis
#'
#' @description Generate a Virdis Brewer palette of a given size
#' @param value.count Number of colors to generate; min is 3 (default); max is 9
#' Get colors from viridis: Colorblind-Friendly Color Maps for R
#' . See virdis::virdis()
#' @return List of palette colors
#' @examples
#' paletteColorVirdis()

#' @export
paletteColorVirdis <- function(value.count = 3) {
    if (value.count == 3) {
        return(c("#440154", "#21908C", "#FDE725"))
    } else if (value.count == 4) {
        return(c("#440154", "#31688E", "#35B779", "#FDE725"))
    } else if (value.count == 5) {
        return(c("#440154", "#3B528B", "#21908C", "#5DC863", "#FDE725"))
    } else if (value.count == 6) {
        return(c("#440154", "#414487", "#2A788E", "#22A884", "#7AD151", "#FDE725"))
    } else if (value.count == 7) {
        return(c("#440154", "#443A83", "#31688E", "#21908C", "#35B779", "#8FD744", "#FDE725"))
    } else if (value.count == 8) {
        return(c("#440154", "#46337E", "#365C8D", "#277F8E", "#1FA187", "#4AC16D", "#9FDA3A", "#FDE725"))
    } else if (value.count == 9) {
        return(c("#440154", "#472D7B", "#3B528B", "#2C728E", "#21908C", "#27AD81", "#5DC863", "#AADC32", "#FDE725"))
    } else {
        stop("n too large, allowed maximum for palette Viridis is 9. Returning the palette you asked for with that many colors")
    }
}

# ==============================================================================
# III.a Internal mapping generators
# ------------------------------------------------------------------------------

# Automatic construction of table.column.values for mapping
.autoTableColumnValues<-function(table=NULL,
                                 table.column=NULL,
                                 mapping.type=NULL,
                                 network=NULL,
                                 base.url=.defaultBaseUrl){
    # Find out all of the values in the named column
    df.values = getTableColumns(table=table, columns=table.column, 
                                network=network, base.url=base.url)
    
    if(mapping.type %in% c('discrete','d','lookup')){
        # Find the frequency distribution, with most common elements first 
        # Note: not same ordering as Cytoscape
        df.freq = table(df.values[table.column])
        
        # Create the mapped values that correspond to the unique elements
        return(names(df.freq))
    } else if (mapping.type %in% c('continuous','c','interpolate')){
        #Determine min and max
        max.value <- max(df.values,na.rm=TRUE)
        min.value <- min(df.values,na.rm=TRUE)
        if(sign(max.value) == sign(min.value)){ #one-tailed; seq
            mid.value = min.value + (max.value - min.value)/2
            return(c(min.value,mid.value,max.value))
        } else {  #two-tailed; div
            #Find max abs value
            max.max.value <- max(max.value, abs(min.value))
            return(c(-max.max.value, 0, max.max.value))
        }
    } else {
        stop("Automatic palette mapping doesn't work for passthrough mappings.")
    }
}

# Internal function to generate a color map
# param table Node, Edge or Network table
# param table.column Name of column
# param color.palette Name of palette function (without quotes)
# param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#  default is continuous
# param network (optional) Name or SUID of the network. Default is the 
#  "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
#  port or version to connect to the CyREST API. Default is 
#  http://localhost:1234 and the latest version of the CyREST API supported by 
#  this version of RCy3.
# return A named list of lists providing a mapping of column values and colors
.genColorMap<-function(table=NULL,
                      table.column=NULL,
                      color.palette=NULL,
                      mapping.type=NULL,
                      network=NULL,
                      base.url=.defaultBaseUrl){

    table.column.values <- .autoTableColumnValues(table, table.column,
                                                  mapping.type,network, base.url)
    colors <- color.palette(length(table.column.values))
    
    return (list('table.column.values'=table.column.values, 'colors'=colors))
}


# ------------------------------------------------------------------------------
# Internal function to generate an opacity map
# param table Node, Edge or Network table
# param table.column Name of column
# param opacities Range of opacity values to work with; default is 50-255
# param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#  default is continuous
# param network (optional) Name or SUID of the network. Default is the 
#  "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
#  port or version to connect to the CyREST API. Default is 
#  http://localhost:1234 and the latest version of the CyREST API supported by 
#  this version of RCy3.
# return A named list of lists providing a mapping of column values and opacities
.genOpacityMap<-function(table=NULL,
                           table.column=NULL,
                           opacities=NULL,
                           mapping.type=NULL,
                           network=NULL,
                           base.url=.defaultBaseUrl){
    table.column.values <- .autoTableColumnValues(table, table.column,
                                                  mapping.type,network, base.url)
    if(is.null(opacities))
        opacities <- c(50,255) #default range
    if(length(opacities) > 2){
        warning("More than 2 opacity values provided. Only using min and max.")
        opacities <- c(min(opacities), max(opacities))
    }else if (length(opacities) < 2){
        stop("Please provide min and max opacity values between from 0 to 255")
    }
    
    opacities <- seq(min(opacities), max(opacities), along.with = table.column.values)
    
    return (list('table.column.values'=table.column.values, 'opacities'=opacities))
}


# ------------------------------------------------------------------------------
# Internal function to generate a dimensions map
# param table Node, Edge or Network table
# param table.column Name of column
# param dims Range of dimension values to work with; default is 10-100
# param mapping.type (char) continuous, discrete or passthrough (c,d,p); 
#  default is continuous
# param network (optional) Name or SUID of the network. Default is the 
#  "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
#  port or version to connect to the CyREST API. Default is 
#  http://localhost:1234 and the latest version of the CyREST API supported by 
#  this version of RCy3.
# return A named list of lists providing a mapping of column values and 
#   dimension values
.genDimMap<-function(table=NULL,
                     table.column=NULL,
                     dims=NULL,
                     mapping.type=NULL,
                     network=NULL,
                     base.url=.defaultBaseUrl){
    
    table.column.values <- .autoTableColumnValues(table, table.column,
                                                  mapping.type,network, base.url)
    if(is.null(dims))
        dims <- c(10,100) #default range
    if(length(dims) > 2){
        warning("More than 2 dimension values provided. Only using min and max.")
        dims <- c(min(dims), max(dims))
    }else if (length(dims) < 2){
        stop("Please provide min and max dimension values.")
    }
    
    dims <- seq(min(dims), max(dims), along.with = table.column.values)
    
    return (list('table.column.values'=table.column.values, 'dims'=dims))
    }


# ------------------------------------------------------------------------------
# Internal function to generate a line style map
# param table.column Name of column
# param network (optional) Name or SUID of the network. Default is the 
#  "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
#  port or version to connect to the CyREST API. Default is 
#  http://localhost:1234 and the latest version of the CyREST API supported by 
#  this version of RCy3.
# return A named list of lists providing a mapping of column values and line 
#  styles
.genLineStyleMap<-function(table.column=NULL,
                           network=NULL,
                           base.url=.defaultBaseUrl){
    
    table.column.values <- .autoTableColumnValues('edge', table.column,
                                                  'd',network, base.url)
    value.count <- length(table.column.values)
    
    if(value.count > 16)
        stop("A maximum of 16 line styles are available.")

    line.styles <- getLineStyles()[seq_len(value.count)]
    
    return (list('table.column.values'=table.column.values, 'line.styles'=line.styles))
}
    
# ------------------------------------------------------------------------------
# Internal function to generate an arrow shape map
# param table.column Name of column
# param network (optional) Name or SUID of the network. Default is the 
#  "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
#  port or version to connect to the CyREST API. Default is 
#  http://localhost:1234 and the latest version of the CyREST API supported by 
#  this version of RCy3.
# return A named list of lists providing a mapping of column values and arrow
#  shapes
.genArrowMap<-function(table.column=NULL,
                       network=NULL,
                       base.url=.defaultBaseUrl){
    
    table.column.values <- .autoTableColumnValues('edge', table.column,
                                                  'd',network, base.url)
    value.count <- length(table.column.values)
    
    if(value.count > 22)
        stop("A maximum of 22 ArrowShapes are available.")
    
    shapes <- getArrowShapes()[seq_len(value.count)]
    
    return (list('table.column.values'=table.column.values, 'shapes'=shapes))
}

# ------------------------------------------------------------------------------
# Internal function to generate a shape map
# param table.column Name of column
# param network (optional) Name or SUID of the network. Default is the 
#  "current" network active in Cytoscape.
# param base.url (optional) Ignore unless you need to specify a custom domain,
#  port or version to connect to the CyREST API. Default is 
#  http://localhost:1234 and the latest version of the CyREST API supported by 
#  this version of RCy3.
# return A named list of lists providing a mapping of column values and shapes
.genShapeMap<-function(table.column=NULL,
                       network=NULL,
                       base.url=.defaultBaseUrl){
    
    table.column.values <- .autoTableColumnValues('node', table.column,
                                                  'd',network, base.url)
    value.count <- length(table.column.values)
    
    if(value.count > 9)
        stop("A maximum of 9 shapes are available.")
    
    shapes <- getNodeShapes()[seq_len(value.count)]
    
    return (list('table.column.values'=table.column.values, 'shapes'=shapes))
}
cytoscape/RCy3 documentation built on April 7, 2024, 2:17 p.m.

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