Additional Documentation page text for v1.2

[kdahlquist]

We need some additional text for the Documentation page because of the new features for v1.2. Please add/edit the following:

• In Section 1, add a new bullet point below the first bullet that reads: "If you do not have your own input spreadsheet, you can load and view demonstration gene regulatory networks. Selecting the menu item Demo > Demo #1: Unweighted GRN will load a network graph with black edges and regular arrowheads. Selecting the menu item Demo > Demo #2: Weighted GRN will load a network graph with edges of varying thicknesses and colored . See Section 3 [link] for details on how GRNsight displays the graph."
• In Section 1, square bullet point 6, after the sentence "The edges will be black with regular arrowheads." add the sentence: The demonstration file "Demo #1: Unweighted GRN" corresponds to the adjacency matrix shown below.
• In Section 1, square bullet point 7, after the sentence " The screenshot below gives an example of this type of adjacency matrix." add the sentence: The demonstration file "Demo #2: Weighted GRN" corresponds to the adjacency matrix shown below.
• In Section 2, add a new bullet point at the bottom of the list that says: If you do not have your own input spreadsheet, you can load and view demonstration gene regulatory networks. Selecting the menu item Demo > Demo #1: Unweighted GRN will load a network graph with black edges and regular arrowheads. Selecting the menu item Demo > Demo #2: Weighted GRN will load a network graph with edges of varying thicknesses and colored . See Section 3 [link] for details on how GRNsight displays the graph.
• In section 3, square bullet point 4, replace the current text with: The color of the edge also imparts information about the regulatory relationship. Edges with positive normalized weight values from 0.05 to 1 are colored magenta; edges with negative normalized weight values from -0.05 to -1 are colored cyan. Edges with normalized weight values between -0.05 and 0.05 are colored grey to emphasize that their magnitude is near zero and that they have a weak influence on the target gene.

[Note that GitHub interpreted the # symbol above as references to other issues; I meant them as what it actually says in the Demo menu.

[kdahlquist]

Some more changes:

Section 3, second set of square bullet points, replace text with:

• Link Distance [make "Link Distance" bold] determines the minimum distance maintained between nodes, i.e., it changes the length of the edges, smaller numbers specify shorter lengths, larger numbers specify longer lengths. The range of values for this parameter are 1 to 1000 with a default value of 500.
• Charge [make "Charge" bold] changes the strength of the force that causes the nodes to repel each other. A more negative value causes more repulsion between nodes. The range of values for this parameter are -2000 to 0 with a default value of -1000.
• Charge Distance [make "Charge Distance" bold] changes the size of the charged area around a node. The larger the number, the larger the size of the charged area around a node that repels other nodes. The range of values for this parameter is 0 to 2000 with a default value of 1000.
• Gravity [make "Gravity" bold] determines the strength of the force holding the nodes to the center of the graph. It varies from 0 (no force) to 1 (maximum force holding the nodes in the center). The default value of this parameter is 0.10.
• You may change the values of each of the force graph parameters by moving the sliders back and forth.
• Checking the box next to “Lock Force Graph Parameters” locks the current settings of the parameters (positions of the sliders) in place so that they cannot be changed. Unchecking the box unlocks the sliders again. Alternately, you can select the menu item Format > Lock Force Graph Parameters to lock the current settings. A check mark will appear next to the menu item to indicate that they are locked. Selecting the menu item Format > Lock Force Graph Parameters a second time will unlock the sliders again.
• Clicking the “Reset Force Graph Parameters” button will restore the default settings. Alternately, you can select the menu item Format > Reset Force Graph Parameters to restore the default settings.
• Clicking the "Undo Reset" button will restore the Force Graph Parameter settings that were in place before the Force Graph Parameters were reset either by clicking the button or selecting the menu item. "Undo Reset" is also a menu item under the Format menu.
• Note that reloading the input file with the same Force Graph Parameter settings (even the defaults) will not necessarily lead to the exact same layout of the graph due to some randomness in D3’s layout algorithm.

[NAnguiano]

The above changes should all be added to the documentation.

[kdahlquist]

Confirmed that changes were made. Am closing now.