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enhancedGraphics

App to add enhanced node graphics to Cytoscape 3.

This documentation is valid for enhancedGraphics version 1.5.4.

Presentation

The enhancedGraphics app adds a set of visual style passthrough mappings for node custom graphics. These mappings are all of the form:

type: argument1="val1" argument2="val2" ...

where type is the type of chart or gradient and the arguments are the instructions for constructing that chart or graphic. Adding the desired mappings to a column in the default node table, and creating a style that utilizes that column to passthrough to one of the Custom Graphics visual attributes will add that graphic to the node referenced by that row in the node table. Note that there is no requirement that nodes have the same mapping or even the same type of mapping. Each of the individual types and their arguments are explained below.

Types

Bar

Paints a bar chart onto the node, according to the arguments provided.

Arguments

  • attributelist String (required*)

    Comma-separated list of node table columns that contain the values for the bars. The type of the table columns should be Double.

  • valuelist String (required*)

    Comma-separated list of the values for the bars. This is ignored if attributelist is given.

  • colorlist String - Default: contrasting

    The color list of each bar or the scaling colors.

  • range String

    Minimum and maximal value of the bars. The string should be formatted as follows: min,max, where min and max are floating points.

  • scale Double - Default: 1.0

    Scale to apply to the whole chart.

  • showyaxis Boolean - Default: false

    Should the y axis be displayed?

  • ybase Double - Default: 0.5

    The vertical base of the chart as a proportion of the height. By default, this is 0.5 (the center of the node), to allow for both positive and negative values. If, however, you only have positive values, you might want to set this to 1.0 (the bottom of the node). Note that this goes backwards from what might be expected, with 0.0 being the top of the node and 1.0 being the bottom of the node. The keywords bottom, middle and top are also supported.

  • separation Integer - Default: 0

    The separation between any two bars.

  • bordercolor String - Default: black

    The single color of the bar borders.

  • borderwidth Double - Default: 0.1

    Width of the bar borders.

  • labellist String - Default: the attributelist is used

    Comma-separated list of the labels. If one label has a comma, it should be escaped as the follows: \\\,. If no labellist is given, the labels will be the name of the attributes.

  • showlabels Boolean - Default: true

    Should the labels be printed?

  • labelfont String - Default: SansSerif

    Font family of the labels.

  • labelsize Integer - Default: 8

    Font size of the labels.

  • labelstyle String - Default: plain

    Font style of the labels. Must be one of:

    • plain
    • italics
    • bold
    • bolditalic

  • labelcolor String - Default: black

    The single color of the labels.

  • labelwidth Double

    Maximal width that a label should have. The unit is the same as node sizes. If the text is to long to fit, new lines are created so that the text fit in the width. If labelwidth is not given, the label will be on one line.

  • labelspacing Double - Default: 1.0

    In case the label is on several lines, this is the size of the space between two lines. The unit is the same as node sizes.

* at least one of the arguments is required.

Examples

  • barchart: attributelist="a,b,c,d" colorlist="up:yellow,down:green"

    In this example, the values of a,b,c, and d are 2.0, 0.5, 4.0, and -1.0. Because no range is given, the positive values are yellow and the negative value is green.

  • barchart: valuelist="4,5,3" labellist="A,B,C" ybase="bottom" showyaxis=true separation=4 range="2.5,5"

    In this example, the values are all positives, so we place the chart at the bottom of the node. To emphasize on the difference between the bars, we zoom on the area [2.5,5] of the chart and display the Y axis.

barchart screenshot

List of types

Circos

This chart type displays the values passed as arguments as a concentric circles with portions of the circle (slices) divided according to the values provided.

Arguments

  • attributelist String (required*)

    Comma-separated list of node table columns that contain the values for the slices. The type of the table columns should be List of Double. The chart will have as many circles as attributes. All attributes are list of floating points, and they must have the same number of elements.

    If no valuelist is given, an attribute will be considered as a value. In this case, the attributes will represent the size of a slice and thus must be positive.

  • valuelist String (required*)

    Represent the size of slices. The values should be positive.

    The valuelist argument can be:

    • a comma-separated list of positive floating points, all the circles will have the same slice sizes.

    • a list of comma-separated list of values formatted as follows: [circle1_slice1,circle1_slice2,circle1_slice3],[circle2_slice1,circle2_slice2,circle2_slice3] where circleX_sliceY is a positive floating point value representing the size of the given slice from the given circle.

      Note: The values of each circle are independent, they represent a proportion of the slice in the circle. For example, [2,2,2],[3,3,3] is equivalent to 1,1,1 even if the values are different, they represent the same proportion.

      The first circle is the inner circle, the last circle is the outer circle.

    If no valuelist is given, the attributelist will be treated as a valuelist.

  • colorlist String - Default: contrasting

    The colorlist argument can be:

    • a color list or scaling colors defining the color scheme for all the slices of all circles.
    • a list of color schemes formatted as follow: [color_circle1],[color_circle2] where color_circleX is a color list or scaling colors for the specific circle. It means that each circle can have a different color scheme.

  • range String

    Minimum and maximal value of the slices. The string should be formatted as follows: min,max, where min and max are floating points.

  • arcstart Double - Default: 0.0

    The angle in degrees to start the slices. 0 points east, 90 points north, etc.

  • arcdirection String - Default: counterclockwise

    The direction in which the slices are drawn. Must be one of:

    • clockwise, clock, cw: the slices are drawn clockwise.
    • counterclockwise, anticlockwise, ccw, acw: the slices are drawn anti-clockwise.

  • firstarc Double - Default: 0.2

    Where to begin the first circle, as a proportion of the entire node. 0 means that the first circle is a pie. 1 means that the first circle is around the node.

  • arcwidth Double - Default: 0.1

    The width of each circle but the first, as a proportion of the entire node. The default value 0.1 means that the arc width is equals to 10% of the node width.

  • firstarcwidth Double - Default: 0.1

    The width of the first circle, as a proportion of the entire node. The default value 0.1 means that the arc width is equals to 10% of the node width.

  • bordercolor String - Default: black

    The single color of the slice borders.

  • borderwidth Double - Default: 0.1

    Width of the slice borders.

  • labellist String

    Comma-separated list of the slice labels. Only the outer circle will have the labels. If one label has a comma, it should be escaped as the follows: \\\,.

  • showlabels Boolean - Default: false

    Should the slice labels be printed?

  • circlelabels String

    Comma-separated list of the circle labels. If one label has a comma, it should be escaped as the follows: \\\,.

  • labelcircles String

    The position of the circle labels. Must be one of:

    • east
    • west

  • labelfont String - Default: SansSerif

    Font family of the labels.

  • labelsize Integer - Default: 8

    Font size of the labels.

  • labelstyle String - Default: plain

    Font style of the labels. Must be one of:

    • plain
    • italics
    • bold
    • bolditalic

  • labelcolor String - Default: black

    The single color of the labels.

  • labelwidth Double

    Maximal width that a label should have. The unit is the same as node sizes. If the text is to long to fit, new lines are created so that the text fit in the width. If labelwidth is not given, the label will be on one line.

  • labelspacing Double - Default: 1.0

    In case the label is on several lines, this is the size of the space between two lines. The unit is the same as node sizes.

* at least one of the arguments is required.

Examples

  • circoschart: attributelist="list_a,list_b,list_c" colorlist="up:yellow,down:green" labellist="node 1\\\, slice 1,node 1\\\, slice 2,node 1\\\, slice 3,node 1\\\, slice 4" firstarc=1 arcwidth=.3 valuelist="1,1,1,1"

    In this example, the values of list_a, list_b, and list_c are [1.0,2.0,3.0,4.0], [-5.0,3.0,-2.0,1.0], and [-1.0,-2.0,-3.0,-4.0]. Because the values are equals, the circles will be split into four same-sized slices. No range given, so the positive values will be yellow and the negative values will be green. The slices are labelled, the labels will point to the outer circle. The chart will be around the node (firstarc=1) and the width of the circles is increased compared to the default value.

    We can note that the chart fits to the node, even if it is not square (or round). In this configuration the chart is an ellipse.

  • circoschart: attributelist="list_a,list_b,list_c" colorlist="up:yellow,zero:white,down:green,missing:black" labellist="slice 1,slice 2,slice 3,slice 4" firstarc=1 arcwidth=.3 valuelist="1,1,1,1" range="-5,5" arcdirection="clockwise"

    In this example, the values of list_a, list_b, and list_c are [1.0,2.0,3.0,4.0], [-5.0,NaN,-2.0,1.0], and [-1.0,-2.0,-3.0,-4.0]. Because the values are equals, the circles will be split into four same-sized slices. With the range, the colors will scale from green to white or white to yellow depending of the sign of the value, and a missing value will be painted black. Here the slices are drawn clockwise (starting at 3 o'clock by default).

  • circoschart: attributelist="list_a,list_b,list_c" circlelabels="a,b,c" labelcircles="east" firstarc=.1 arcwidth=.3 arcstart=90

    In this example, the values of list_a, list_b, and list_c are [1.0,2.0,3.0,4.0], [5.0,3.0,2.0,1.0], and [10.0,6.0,3.0,1.0]. Because there is no value, the attributes are used as values. The default colors are contrasting, in this case the colors are, in order: red, purple, cyan and lime. Here the labels are not for the slices but for the circles, they will be drawn on the right side of the node. The starting point of the slice will be 12 o'clock (arcstart=90) and drawn counterclockwise by default. The widths (firstarc and arcwidth) are calculated so that the chart is inside the node that was previously shaped as a circle.

  • circoschart: valuelist="[1,2,3],[2,1,4]" colorlist="[red,red,darkgreen],[darkgreen,red,black]" firstarc=.7 arcwidth=.3 bordercolor=white borderwidth=1

    In this example we manually give the values and colors for each slice of each circle. We have chosen dark colors, so we use a bright border color, and increased its width compared to default.

circoschart screenshot

List of types

Heatstrip

This chart type displays the values passed as arguments as a bar chart with the bars showing a gradient between the center and upper and lower values.

Arguments

  • attributelist String (required*)

    Comma-separated list of node table columns that contain the values for the bars. The type of the table columns should be Double.

  • valuelist String (required*)

    Comma-separated list of the values for the bars. This is ignored if attributelist is given.

  • colorlist String - Default: yellowblackcyan

    A scaling color, or one of the following keywords:

    • bluegreenyellow
    • greenpurple
    • orangepurple
    • purpleyellow
    • redblue
    • redgreen
    • redyellow
    • yellowblue
    • yellowcyan
    • yellowblackcyan
    • yellowwhitecyan

    Note: If you define a scaling color using only up and down, the zero will be black by default. By using a keyword color with only two colors, the gradient will scale from one to another without using a default middle color.

  • range String

    Minimum and maximal value of the bars. The string should be formatted as follows: min,max, where min and max are floating points.

  • scale Double - Default: 1.0

    Scale to apply to the whole chart.

  • separation Integer - Default: 0

    The separation between any two bars.

  • bordercolor String - Default: black

    The single color of the bar borders.

  • borderwidth Double - Default: 0.1

    Width of the bar borders.

  • labellist String - Default: the attributelist is used

    Comma-separated list of the labels. If one label has a comma, it should be escaped as the follows: \\\,. If no labellist is given, the labels will be the name of the attributes.

  • showlabels Boolean - Default: true

    Should the labels be printed?

  • labelfont String - Default: SansSerif

    Font family of the labels.

  • labelsize Integer - Default: 8

    Font size of the labels.

  • labelstyle String - Default: plain

    Font style of the labels. Must be one of:

    • plain
    • italics
    • bold
    • bolditalic

  • labelcolor String - Default: black

    The single color of the labels.

  • labelwidth Double

    Maximal width that a label should have. The unit is the same as node sizes. If the text is to long to fit, new lines are created so that the text fit in the width. If labelwidth is not given, the label will be on one line.

  • labelspacing Double - Default: 1.0

    In case the label is on several lines, this is the size of the space between two lines. The unit is the same as node sizes.

* at least one of the arguments is required.

Examples

In the following examples, the values of the attributes a, b, c, and d are 1.0, 2.0, 3.0, -3.0 respectively.

  • heatstripchart: attributelist="a,b,c,d" showyaxis=true

    In this example we use the default values, except that we add the Y axis to see the limits of the values.

  • heatstripchart: attributelist="a,b,c,d" colorlist="yellowcyan" showyaxis=true separation=2 showlabels=false

    In this example we change the color scheme, the only difference is the zero color which by default is black and here is not used, meaning that the zero color is the mix between up and down, here lime is the mix between yellow and cyan. We get rid of the labels and we add some space between the bars.

heatstripchart screenshot

List of types

Label

This chart type provides a mechanism to add text labels to nodes that have more display options than the simple labels provided by Cytoscape visual properties.

Arguments

  • attribute String (required*)

    Node table column that contain the text of the label.

  • label String (required*)

    The text of the label. This is ignored if attribute is given.

  • labelAlignment String - Default: middle

    The way the label should be aligned according to the position. Must be one of:

    • none: position is at the top left corner of the label.
    • left: position is on the left of the label.
    • center, center_top: position is on top of the label, centered horizontally.
    • center_bottom: position is at the bottom of the label, centered horizontally.
    • right: position is at the right of the label.
    • middle: position is at the middle of the label.

  • position String - Default: center

    Where the label position should be calculated from. The string can be formatted as x,y or one of the following keyword:

    • center: the middle of the node
    • north: the top border of the node, centered horizontally
    • northeast: the top-right corner of the node
    • east: the right border of the node, centered vertically
    • southeast: the bottom-right corner of the node
    • south: the bottom border of the node, centered horizontally
    • southwest: the bottom-left corner of the node
    • west: the left border of the node, centered vertically
    • northwest: the top-left corner of the node

  • anchor String - Default: center

    Where the label text should be anchored. The string can be formatted as x,y or one of the following keyword:

    • center: the middle of the text
    • north: the top border of the text, centered horizontally
    • northeast: the top-right corner of the text
    • east: the right border of the text, centered vertically
    • southeast: the bottom-right corner of the text
    • south: the bottom border of the text, centered horizontally
    • southwest: the bottom-left corner of the text
    • west: the left border of the text, centered vertically
    • northwest: the top-left corner of the text

  • labeloffset String - Default: 0,0

    The offset of the label. The string should be formatted as follows: x,y, where x is the horizontal offset and y the vertical offset.

  • labelfont String - Default: SansSerif

    Font family of the labels.

  • labelsize Integer - Default: 8

    Font size of the labels.

  • labelstyle String - Default: plain

    Font style of the labels. Must be one of:

    • plain
    • italics
    • bold
    • bolditalic

  • color String - Default: black

    The single color of the labels.

  • labelwidth Double

    Maximal width that a label should have (paddings included). The unit is the same as node sizes. If the text is to long to fit, new lines are created so that the text fit in the width. If labelwidth is not given, the label will be on one line.

  • labelspacing Double - Default: 1.0

    In case the label is on several lines, this is the size of the space between two lines. The unit is the same as node sizes.

  • padding Double - Default: 0.0

    Proportion of the node's width to be used as a padding.

  • background Boolean - Default: false

    Should a background be drawn?

  • bgColor String - Default: white

    The single color used as the background. The background is transparent.

  • outline Boolean - Default: false

    Should the letters be outlined?

  • outlineColor String - Default: black

    The single color of the outline.

  • outlineTransparency Integer

    The transparency of the outline. Should be an integer between 0 and 255.

  • outlineWidth Double - Default: 0.0

    Width of the outlines.

* at least one of the arguments is required.

Examples

  • label: label="This is text"

    Default values are used: the text is centered in the middle of the node.

  • label: attribute="long_text" labelwidth=75 background=true bgColor=red padding=0.05

    In this example, the text of the label is read from the attribute long_text, which value is This is a text on several lines. To make the label on several lines, we put a maximum width (the node width is 75). To emphasize the label we put a red background. To increase readability, we add a padding so that letters are not too close to the node borders.

  • label: label="This is text is on several lines" labelwidth=75 position="northwest" labelAlignment="left" padding=0.05

    In this example we show how to put a text which is not centered. We put the text on the top-left corner and we align the text with the right border.

  • label: label="This is text" position="south" labelAlignment="center_top" anchor="north"

    In this example the label leaves the node. We want it to be below the node, so we want the north of the label to be at the south of the node.

label screenshot

List of types

Line

This chart type displays the values passed as arguments as a line chart on the node.

Arguments

  • attributelist String (required*)

    Comma-separated list of node table columns that contain the values for the points. The type of the table columns should be Double.

  • valuelist String (required*)

    Comma-separated list of the values for the points. This is ignored if attributelist is given.

  • colorlist String - Default: contrasting

    A color for the line, or a color list for each line between two points. It is also possible to give a scaling color, each line between two points will be painted with the up color if the difference is positive, or with the down if the difference is negative.

  • linewidth Double - Default: 1.5

    Width of the line

* at least one of the arguments is required.

Examples

  • linechart: attributelist="a,b,c,d" colorlist="up:red,down:blue"

    In this example, the attribute values of a, b, c and d are 2.0, 0.5, 4.0, and -1.0 respectively. The colors of the line will depend on the difference between the two points: if it decreases it will be blue, if it increases it will be red.

  • linechart: valuelist="1,4,2,3,0" colorlist="green"

    In this example, the values are manually given and the line will have only one color.

linechart screenshot

List of types

Linear Gradient

This chart type displays a linear gradient on the node.

Arguments

  • start String (required)

    The starting coordinate of the gradient. This must be formatted as follows: x,y.

    The point 0,0 is the top-left corner of the node. The point 1,0 is the top-right corner of the node. The point 1,1 is the bottom-right corner of the node. The point 0,1 is the bottom-left corner of the node.

  • end String (required)

    The ending coordinate of the gradient. This must be formatted as follows: x,y.

    The point 0,0 is the top-left corner of the node. The point 1,0 is the top-right corner of the node. The point 1,1 is the bottom-right corner of the node. The point 0,1 is the bottom-left corner of the node.

  • stoplist String (required)

    List of stops separated with a vertical bar |. A stop is a comma-separated list of a color and the proportional distance, formatted as follows: r,g,b,a,s or r,g,b,s where

    • r is the red-component of the color (Integer in the range [0,255]);
    • g is the green-component of the color (Integer in the range [0,255]);
    • b is the blue-component of the color (Integer in the range [0,255]);
    • a is the alpha or opacity of the color (Integer in the range [0,255]);
    • s is the distance of the stop (Double in the range [0.0,1.0]) where 0.0 is the beginning of the gradient and 1.0 is the end of the gradient.

Examples

  • lingrad: start="0,1" end="1,0" stoplist="0,0,255,255,0.0|255,255,255,255,0.5|255,0,0,255,1.0"

    In this example, we want a linear gradient that follows the diagonal from the bottom-left corner to the top-right corner. We want the starting color to be blue, then in the middle it will be white and at the end it is red.

  • lingrad: start="0,0" end="1,0" stoplist="0,0,255,255,0.0|0,255,255,255,0.25|255,255,0,255,0.75|255,0,0,255,1.0"

    In this example, the gradient follows the horizontal line. We have four colors in the gradient.

lingrad screenshot

List of types

Pie

This chart type displays the values passed as arguments as a pie chart on the node.

Arguments

  • attributelist String (required)

    attributelist can be two different things:

    • A node table column that contain the values for the slices. The type of the table column should be List of Double.

    • Comma-separated list of node table columns that contain the values for the slices. The type of the table columns should be Double.

    If no valuelist is given, an attribute will be considered as a value. In this case, the attributes will represent the size of a slice and thus must be positive.

  • valuelist String

    Comma-separated list of positive floating points representing the relative size of the slices.

    If no valuelist is given, the attributelist will be treated as a valuelist.

  • colorlist String - Default: contrasting

    A color list or a semicolon separated list of scaling colors. One can define a color list for the pie, or one can define a scaling color for each attribute of the pie.

  • range String

    Minimum and maximal value of the slices. The string should be formatted as follows: min,max, where min and max are floating points.

  • arcstart Double - Default: 0.0

    The angle in degrees to start the slices. 0 points east, 90 points north, etc.

  • arcdirection String - Default: counterclockwise

    The direction in which the slices are drawn. Must be one of:

    • clockwise, clock, cw: the slices are drawn clockwise.
    • counterclockwise, anticlockwise, ccw, acw: the slices are drawn anti-clockwise.

  • firstarc Double - Default: 0.2

    Where to begin the first circle, as a proportion of the entire node. 0 means that the first circle is a pie. 1 means that the first circle is around the node.

  • arcwidth Double - Default: 0.1

    The width of each circle but the first, as a proportion of the entire node. The default value 0.1 means that the arc width is equals to 10% of the node width.

  • firstarcwidth Double - Default: 0.1

    The width of the first circle, as a proportion of the entire node. The default value 0.1 means that the arc width is equals to 10% of the node width.

  • outlineColor String - Default: black

    The single color of the slice borders.

  • outlineWidth Double - Default: 0.1

    Width of the slice borders.

  • labellist String

    Comma-separated list of the slice labels. Only the outer circle will have the labels. If one label has a comma, it should be escaped as the follows: \\\,.

  • showlabels Boolean - Default: false

    Should the slice labels be printed?

  • circlelabels String

    Comma-separated list of the circle labels. If one label has a comma, it should be escaped as the follows: \\\,.

  • labelcircles String

    The position of the circle labels. Must be one of:

    • east
    • west

  • labelfont String - Default: SansSerif

    Font family of the labels.

  • labelsize Integer - Default: 8

    Font size of the labels.

  • labelstyle String - Default: plain

    Font style of the labels. Must be one of:

    • plain
    • italics
    • bold
    • bolditalic

  • labelcolor String - Default: black

    The single color of the labels.

  • labelwidth Double

    Maximal width that a label should have. The unit is the same as node sizes. If the text is to long to fit, new lines are created so that the text fit in the width. If labelwidth is not given, the label will be on one line.

  • labelspacing Double - Default: 1.0

    In case the label is on several lines, this is the size of the space between two lines. The unit is the same as node sizes.

Examples

  • piechart: attributelist="list_a" labellist="slice 1,slice 2, sclie 3, sclie 4, slice 5"

    In this example, the value of the attribute list_a is [5.0,2.0,3.0,4.0,1.0]. Each slice is labelled and the colors are the default contrasting colors.

  • piechart: attributelist="a,b,c" valuelist="1,1,1" colorlist="up:red,down:blue,zero:white" range="-3,3"

    In this example, the three slices have the same sizes and the colors depends on the values of the attributes a, b and c which values are respectively 2.0, -1 and 4.0. Here because some values are not in the range defined, the color assigned is the same as the limit one, in this case, 4.0 is assigned the up color because it is greater than the max range. The other colors scale from blue to white or white to red.

piechart screenshot

List of types

Radial Gradient

This chart type displays a radial gradient on the node.

Arguments

  • stoplist String (required)

    List of stops separated with a vertical bar |. A stop is a comma-separated list of a color and the proportional distance, formatted as follows: r,g,b,a,s or r,g,b,s where

    • r is the red-component of the color (Integer in the range [0,255]);
    • g is the green-component of the color (Integer in the range [0,255]);
    • b is the blue-component of the color (Integer in the range [0,255]);
    • a is the alpha or opacity of the color (Integer in the range [0,255]);
    • s is the distance of the stop (Double in the range [0.0,1.0]) where 0.0 is the beginning of the gradient and 1.0 is the end of the gradient.

  • center String - Default: 0.5,0.5

    The coordinates of the center of the gradient. This must be formatted as follows: x,y.

    The point 0,0 is the top-left corner of the node. The point 1,0 is the top-right corner of the node. The point 1,1 is the bottom-right corner of the node. The point 0,1 is the bottom-left corner of the node.

  • radius Double - Default: 1

    The radius of the gradient as a proportion of the node size. The size of the node here is the minimum between the height and width of the node.

Examples

  • radgrad: stoplist="0,0,255,255,0.0|255,255,255,255,0.5|255,0,0,255,1.0"

    In this example, we want a radial gradient from blue to white and white to red. The default center is the center of the node. The default value here is the height of the node because the height is smaller than the width.

  • radgrad: center="0,1" radius=2 stoplist="255,255,0,255,0.2|255,127,0,255,0.75|255,0,0,0.9|55,65,170,255,1.0"

    In this example, we want a radial gradient from the bottom-left corner of the node, with a radius twice as large as the height of the node. In this gradient we define four colors with different distances.

radgrad screenshot

List of types

Stripe

This simple chart type displays the values passed as arguments as a series of stripes on the node.

Argument

  • colorlist String (required)

    The color list of each stripes. Here the color list keywords do not work, one can only use a list of single colors.

Examples

  • stripechart: colorlist="#051440,white,#EC1920 "

    In this example we define the French flag.

  • stripechart: colorlist="black,#ffe936,#ff0f21"

    In this example we define the Belgian flag.

stripechart screenshot

List of types

Colors

There are several ways to define a colors with enhancedGraphics. One can use a single color to define the color of a text or a border. It is also possible to define or use predefined color list to fill the color of charts. In the case of continuous attributes, one can also define scaling colors where the color of each chart element is calculated in function of the value.

Single color

In order to define a single color, one can use the hexadecimal code #rrggbb or #rrggbbaa with alpha. It is also possible to use one of the many usual keywords such as black, white, navy, etc.

Color list

There are two types of color list: the user-defined and the keywords.

A user-defined list is a comma-separated string of single colors. The number of colors in the list must fit the number of chart elements to draw.

The app also gives access to four predefined color lists, defined thanks to the following keywords:

  • random: the colors change every time the chart are drawn (every time the view is changed).
  • rainbow: the colors from the rainbow, the first element of the list is red, the last is turquoise. The other elements ranges from red to turquoise so that the number of colors matches the number of chart elements.
  • contrasting: two consecutive colors will be from opposite sides of the color wheel.
  • modulated: same as rainbow but the saturation and intensity change.

Scaling color

If dealing with continuous data, one may want to apply a color scale. The color scales are defined thanks to four different type of colors:

  • up: the color for positive values. (required)
  • down: the color for negative values. (required)
  • zero: the color for zero. Default: black
  • missing: the color for missing values (NA, NaN, null). Default: grey

The string defining the color scale is a comma-separated list of type_of_color:color. The string must at least contains the up and down color types.

Note: Only if the range argument is given the color will be scaled. Otherwise all positive values will be assigned with the up color and all negative values with the down color. With the range argument, the color depends on the value of the attribute and will be scaled from zero to up, if positive, or down, if negative.

Examples:

  • up:red,down:blue
  • up:red,zero:white,down:#0000ff
  • up:darkred,down:navy,zero:white,missing:black

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App to add enhanced node graphics to Cytoscape 3

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