To display a Plate Heat Map:

 

1. Select the Insert→Other Plots→Plate Heat Map command.

2. Click (or click-drag) on your layout where you want the plate heat map to appear.

3. Browse to the data file you wish to insert:

i.If you are loading a list of data files collected together in a microtiter plate (e.g., data files derived from a BD HTS instrument), each file will likely already contain a WellID keyword with the well position for that sample. To open those files as a plate, choose FCS Plate folder from the Files of type drop-down list in the Select a Data File dialog, open the folder that contains the files, choose any individual well's file in that folder, and click Open File.

Note: The folder containing the files should also contain an extra keywords file to indicate the size of the plate, if this information is not already present as keywords in the data files. Ready-to-use extra keywords files indicating the size of the plate can be downloaded from the De Novo Software web site.

ii.If you are loading a single file representing all the wells in a plate (e.g., an Accuri .C6 or .CI file), choose the appropriate file type from the Files of type drop-down list in the Select a Data File dialog (e.g., "BD Accuri .c6 Plate files"), and click Open File. No additional extra keyword files will be required since both the WellID and plate size are likely already contained in the data set.

iii. If you would like to display a heat map for a series of files that have not been acquired in a microtiter plate (i.e. files that contain do not contain a WellID keyword or the plate size), you may do so in the following  ways:

▪If you would like to control the well which the file will be associated with, the folder containing the files should also contain an extra keywords file to indicate the size of the plate and extrakeywordstable.csv file indicating the WellID (or $WellID) column with the well position for each file.

▪If you do not need to control which well the file will be associated with, you can use the Merge FCS Files loader which will load samples into the plate heat map in the order they were selected during the file merge. Setting the number of columns to display will determine the plate format.

iv. If you are visualizing SPADE tree please insert a Plate Heat Map as described in step 1 above and follow the instructions for Working with SPADE transformations.

v. If you are visualizing result of a k-Means clustering please insert a Plate Heat Map as described in step 1 above and follow the instructions for Applying a k-Means cluster analysis.

 

 

The data in a Plate Heat Map is displayed as a two-dimensional grid of the wells on a microtiter plate. For example, for a 96-well plate, the plate heat map contains eight rows (labeled A through H) and 12 columns (labeled 01 through 12). The parameter being displayed is shown as the title of the y-axis. Each well displays a color according to the chosen color scheme, and the well's radius can be dependent upon a chosen parameter (Figure 5.85).

 

You can now create Well Gates to pool your data from multiple wells, and display the parameters of each event on a per-well basis in a Data Grid.

 

 

 

 

 

When a Data Grid is displayed for the Plate Heat Map, a Well column will be present showing the well where each cell or event is located.  The example below is from an image cytometry experiment, where the Data Grid has been formatted as an image gallery (Figure 5.86).

 

 

 

You can insert a table displaying the actual values from each well of your Plate Heat Map into a Text Box. For a 96-well microtiter plate, this will insert an 8 x 12 data grid. To do so, right-click on the Text Box, choose Insert Plate Heat Map Stats Grid, and select the Plate Heat Map to use as a data source from the menu. (Figure 5.87). Tables can be displayed in Grid Layout Stats Grid, Column Order Stats Grid, or Row Order Stats Grid.

 

 

 

Grid Layout Stats Grid - displays the plate heat map well statistics in a table similar to the plate heat map (Figure above).

Column Order Stats Grid - displays the plate heat map well statistics according to the plate column order, ie, A01, B01, C01.... (Figure 5.88)

Row Order Stats Grid - displays the plate heat map well statistics according to the plate row order, ie, A01, A02, A03.... (Figure below)

 

 

 

 

All stats grids may be copied and pasted into Excel or the table dragged into a batch process export action for easy reporting.