Introduction

GSearcher is a cytoscape plugin that offers a high performance searching over complex attribute tables.

Installation

To install, simply put the GSearcher_1.4.jar into cytoscape/plugins/ folder. You may load the plugin from Plugins->GSearcher

The latest build of GSearcher can be downloaded here (Cytoscape 2.7.0+): GSearcher 1.4

We will also submit GSearcher to Cytoscape repository soon.

Usage

  • Initialize GSearcher: To load GSearcher Panel, go to Cytoscape->Plugins->GSearcher
    The GSearcher Panel will be loaded on the South panel, initialized with the attribute data from the current network.
  • Quick Search: For quick search, type in the search box, and result will be displayed interactively in the table. Attribute table cells which match the searching criteria are highlighted as color RED. Columns can be reordered by dragging the column headers, and sorted by single click on the column headers. The users can add/remove columns by clicking the column control button on the top right corner of the table, and check/uncheck columns. The hidden columns are automatically removed from the search pool.
  • Basic Controls: All the control operations can be done with the GSearcher toolbar. Which is shown as follows:

    The functions of control buttons/combos/text fields are listed below, ordered from left to right.

    • Reload Table: Reload the GSearcher Attribute Browser table with the current network data. The user needs to perform this operation if the network attributes have been modified since last search, or changed the current network to a differnt network.
    • Select All Rows: Select all rows in the GSearcher Attribute Browser table, with corresponding nodes either selected in YELLOW or highlighted in GREEN (Explained below).
    • Clear Selection and Highlight: Clear all selected rows from the table. This will not change the selection in the network view, but will clear GREEN highlight from nodes, if any.
    • Copy to Clipboard: Copy selected Rows, Columns or Cells to the clipboard, which can be then copied into the search box by Ctrl+V or pasted into other text editor softwares.
    • Export to File: Export the current attribute table to tsv text file.
    • Selection Mode Combo: A combo box with drop downs Row, Column and Cell. This allows the user to change the selection behavior. Default is Row selection.
    • Static Mode Toggle: This toggle button lets the user switch between interactive mode and static mode. In interactive mode, the attribute table is updated whenever user strikes a key in the search box. In static mode, the attribute table cells highlighting is always updated interactively. The result table is only updated when the user strikes the ENTER key. This allows the user examine rows both matching and not matching the query.
    • Highlight Flag Toggle: By default, GSearcher will set node selection status in the current network view in concordance with the selection status of the attribute table. Depress this toggle button will let GSearcher to highlight nodes corresponding to selected rows in the attribute table to be highlighted GREEN. This enables the user to use GSearcher to identify nodes of interest while preserve the current selection state in the network view.
    • Attribute Mode Combo: This combo allows the user to choose searching from either node attributes or edge attributes.
    • Search Mode Combo: GSearcher provides the user several different searching modes. This is explained in detail below. The examples are drawn from the Cytoscape bundled test data galFiltered.cys. Search terms and matching values are with in quotes ”:
      • Terms Anywhere(M): Match can occur anywhere. Multiple keywords can be supplied at the same time separated by spaces. This search is case insensitive.

        Example:
        'MCM' will match 'MCM', 'MCM_YEAST'

      • Begins with Phrase: Match can only occur at the beginning. Spaces are treated as-is. This search is case insensitive.

        Example:
        'DNA rep' will match 'DNA replication'

      • Reg Exp: Match is tested using regular expression. If there’s a syntax error in the user input, the search box will turn red. A complete regular expression reference can be found here: JAVA Regular Expression, in the paragraph summary of regular-expression consructs. Note that regular expression is case sensitive. To make it insensitive, add “(?i)” as the prefix.

        Example:
        'YNL.*' will match every field begins with 'YNL', such as 'YNL116W', 'YNL154C'
        '^FMP\d+' will match every field begins with 'FMP', followed by any number, such as 'FMP40', 'FMP22', 'FMP16'
        '(?i).*acs2.*' will match every field contains 'acs2', ignoring case, such as 'Acs2p', 'ACS2'

      • Exact: Match can occur only when the field matches exactly to the search term, with white spaces preserved. This search is case insensitive.

        Example:
        'PRE' will only match 'PRE'

      • Exclude Phrase: Match can occur only when the field does NOT contain the search term. This search is case insensitive. Results are highlighted BLUE Example:
        'UNKNOWN' will only match fields which don't contain 'UNKNOWN'

      • Phrase: Match can occur only when the field contains the given phrase, with all white spaces preserved. This search is case insensitive. BLUE.

        Example:
        'ATP binding' will only match fields which contain 'ATP binding'. Fields like 'DNA binding, ... ATPase' will match in 'Terms Anywhere(M)' mode but not in phrase mode.

      • Search Box: This is where the user feeds GSearcher with query terms.
      • Advanced Search Panel Toggle: Toggle advanced search mode. This allows the user to build more sophisticated queries. When advanced mode is activated, the quick search mode is disabled. The user may switch between the advanced mode and simple mode using this toggle button.
      • About button: Display about dialogue.
      • Remove GSearcher: Remove GSearcher Panels from Cytoscape.
  • Advanced Controls: The user may use the Advanced Search Panel Toggle button to bring up advanced filters for more complex queries. The user may add arbitrary number of ‘Text’, ‘Threshold’ and ‘Range’ filters. The user may also define the relationship between filters, either AND, which means all filters need to be satisfied, or OR, at least one of the filters needs to be satisfied.
    • Text Filter: Each of these filters behaves exactly like simple search. Here the user is capable of mixing arbitrary number of filters on specific table fields, such as using regular expression to query one column and using phrase to query another column.
    • Threshold Filter: Each of these filters can threshold a numeric value. The attribute table must be either Integer, Double or Float. The results are displayed in VIOLET.
    • Range Filter: Each of these filters can set range on a numeric value. The attribute table must be either Integer, Double or Float. The results are displayed in VIOLET.

Screenshots from GLay examples

Simple search example. Cytoscape selected nodes are colored yellow. GSearcher selected nodes are colored green. Rows matching the keyword ‘mcm1’ are shown in the browser.

Advanced search example. Select nodes by Expression values, threshold on Degree, all columns with the keyword ‘uniprot’ and Family Description Column with the term ‘ambi’.

References

Cytoscape software foundation
GlazedLists
SwingX

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