Select Matrix
The first step in building a heat map with the NG-CHM Builder is to select a matrix file for the heat map. On this screen the user can open their own file or choose to use a sample file provided with the application. Users may select a matrix and enter information for the new heat map by making selections and entries on the configuration panel.
NG-CHM heat maps require a tab delimited text file containing a matrix of data. The file must have row and column headers with labels that identify the content of the rows/columns and numeric values in the remainder of the matrix. Use the Open Matrix File button to load your matrix. If you don't have a matrix and want to try the application, the Sample Matrix open button may used to open a matrix file that will allow you to explore the features of the application.
Once a matrix file has been selected and opened, the Results Panel will be populated with data from the matrix. The Results Panel on this particular screen of the NG-CHM Builder application differs from other screens in the application in that the user can perform some select configuration tasks in the panel. These allow the user to select locations in the matrix where labels and data are located. Matrix data may begin in a position other than (1,1) in the matrix. Users may select the location of the label row and label column as well as pick a starting point for the matrix data by selecting from the radio buttons above the matrix and then clicking on the displayed matrix itself to make a selection. The colors blue (labels) and green (data) are displayed on the matrix to show your selections. The system default is row 1 column 1 for row and column labels, respectively, and (2,2) for matrix data start location.
Advanced users may choose the option to open a file that contains embedded covariate file data located within the matrix itself. In these cases the covariate data will be represented by rows and columns in the matrix. Controls on the results panel allow the user to select the locations of covariate bars on each axis. The color yellow is displayed on the matrix to show covariate selections. If covariate bars are selected within the matrix, the configuration panel will be expanded to allow users to select the color type (discrete/continuous) for each bar.
Configuration Controls
| Configuration Item | Description of Function |
|---|---|
| Open Matrix File | Press this button to select a data matrix file and begin building the heat map. |
| Try Sample Matrix | Press this button to select the sample data matrix. This matrix can be used to explore all of the features of the NG-CHM Builder. By proceeding through the screens and making configuration selections, you may construct the sample heat map and view it interactively. |
| Show Advanced Features | Check this box to expand builder options to show advanced system features. Uncheck the box to see a streamlined set of standard builder options. |
| Heat Map Name | Enter a Name for the heat map. This name will be displayed in the NG-CHM Viewer and be used as the file name for the map when downloaded. |
| Heat Map Description | Enter a free-form description for the heat map. This description will appear in the NG-CHM Viewer. |
| Pixel Summary Method * | Select a Pixel Summary Method (Mean Value, Sample Value, or Predominant Value). This method will be used to summarize values for pixel representation on the summary panel (left side) of the NG-CHM Viewer. |
| Covariate Color Type * | Select a color type (discrete or continuous) for the titled covariate bar. |
| Labels Row | Select this button to choose the labels row of the matrix by then clicking a row on the grid below. The selected row will be colored blue in the matrix display. |
| Labels Column | Select this button to choose the labels column of the matrix by then clicking a column on the grid below. The selected column will be colored blue in the matrix display. |
| Row Covariates * | Select this button to choose any row covariates embedded in the matrix by then clicking column(s) on the grid below. Selected column(s) will be colored yellow in the matrix display. |
| Column Covariates * | Select this button to choose any column covariates embedded in the matrix by clicking rows(s) on the grid below. Selected rows(s) will be colored yellow in the matrix display. |
| Data Start Location | Select this button to choose choose the row/column position where matrix data begins by then clicking a cell on the grid below. All rows and columns to the right and below this position will be colored green in the matrix display. |
| Next | Press this button to proceed to the next screen: Transform Matrix. |
| * - denotes advanced feature configuration options. |
Next Step
Once a matrix has been selected and all required data entered, the user may move on to the next step in the NG-CHM Builder heat map creation process: Transform Matrix.