Plate Heatmap Viewer

HCS-Tools for KNIME version 3.1.200.v201807180901 by Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

Creates trellis of heatMaps to explore your screen. By default nodes expects three columns to be present in order to reorder wells back into plates:
- barcode
- plateRow
- plateColumn

Supported microtiter plate formats:
6, 12, 24, 96, 384 and 1536. The viewer will try to make a guess about the proper plate dimension if not all wells are present in the table (e.g. because outer rows are not used).

Image data:
Tables containing images allow visualization of the well images in the well detail view. Any cell of an image data column will be visualized. So far the KNIME native PNG images are recognised, as well as the formats provided by the Image Processing plugin. Careful! the processing might take time and disk space. The best performance is achieved with the "Image Reference" produced by the "Image File Linker" node of the image processing plugin.

Options

Readouts

A selection of readouts which should be displayed by the viewer. Especially for high-content screens with many readouts (100+), you may want to include just a subset them. This will help to prevent memory problems.

Factors

Annotation column that further characterize the wells.

Barcode

Select column to assign barcode (string or integer).

Row

Select column to assign row value (integer, 1 to 16 refers to A to P).

Column

Select column to assign column value (integer, 1 to 24).

Plate Label

Column that is used to extract the plate label, which should allow easy identification of the plate.

Controls

The subset column allows to choose a nominal attribute, which allows to identify control populations.
Select one ore several reference groups. These can be used to define custom color maps (gray out or mark the populations range with a special color).

Input Ports

A table containing High Content Screening data.

Output Ports

Same as input table.

PNG image of the heatmap trellis containing all plates. It takes the first readout in the list, the default colormap and no overlay.

Views

Plate Heatmap Trellis

Trellis containing all heatmaps representing the plates of the screen.

Mouse behaviour:
The heatmap trellis and the individual plate view support single selection and drag-selection.
Right click on a plate of the trellis opens an individual plate view. A right click on a well of the plate view opens an a well detail view.

Best Friends (Incoming)

• Expand Well Position (9 %) Manipulator
• GroupBy (8 %) Manipulator
• Column Rename (7 %) ManipulatorStreamable
• Row Filter (5 %) ManipulatorStreamable
• String To Number (3 %) ManipulatorStreamable
• Nominal Value Row Filter (3 %) ManipulatorStreamable
• Normalize Plates (POC) (3 %) Manipulator
• Plate Heatmap Viewer (3 %) Visualizer
• CSV Reader (3 %) Source
• File Reader (3 %) SourceStreamable
• Concatenate (3 %) ManipulatorStreamable
• Row Splitter (3 %) ManipulatorStreamable
• Reference Row Filter (3 %) Manipulator
• Joiner (3 %) Manipulator
• Join Layout (2 %) Manipulator
• Normalize Plates (Z-Score) (2 %) Manipulator
• Outlier Removal (2 %) Source
• Table Reader (2 %) SourceStreamable
• Loop End (2 %) LoopEnd
• Number To String (2 %) Manipulator
• Linear Correlation (2 %) Other
• Missing Value (2 %) Manipulator
• Sorter (2 %) Manipulator
• String Manipulation (2 %) ManipulatorStreamable
• Math Formula (2 %) ManipulatorStreamable
• Create Well Position (< 1 %) Manipulator
• Normalize Plates (B-Score) (< 1 %) Manipulator
• Normalize Plates (NPI) (< 1 %) Manipulator
• CV (< 1 %) Manipulator
• Java Snippet (< 1 %) ManipulatorStreamable
• Column List Loop Start (< 1 %) LoopStart
• Hierarchical Clustering (DistMatrix) (< 1 %) Learner
• Concatenate (Optional in) (< 1 %) ManipulatorStreamable
• Cell Splitter By Position (< 1 %) ManipulatorStreamable
• Column Merger (< 1 %) ManipulatorStreamable
• Column Rename (Regex) (< 1 %) ManipulatorStreamable
• Column to Grid (< 1 %) Manipulator
• Constant Value Column (< 1 %) ManipulatorStreamable
• Domain Calculator (< 1 %) Manipulator
• Column Filter (< 1 %) ManipulatorStreamable
• Normalizer (< 1 %) Manipulator
• Pivoting (< 1 %) Manipulator
• RowID (< 1 %) ManipulatorStreamable
• Numeric Row Splitter (< 1 %) Manipulator
• Set Operator (< 1 %) Other
• Unpivoting (< 1 %) Manipulator
• Rule Engine (< 1 %) PredictorStreamable
• Scatter Plot (< 1 %) Visualizer
• Color Manager (< 1 %) Visualizer
• Distance Matrix Calculate (< 1 %) Manipulator
• XLS Reader (< 1 %) SourceDeprecated
• Excel Reader (XLS) (< 1 %) SourceStreamable
• Frequency Filter (< 1 %) Manipulator
• Plate Row Converter (< 1 %) Manipulator
• BinningAnalysis (< 1 %) Manipulator
• Vector Length Normalization (< 1 %) Manipulator
• Z-Primes (PC x NC) (< 1 %) Manipulator
• Split Collection Column (< 1 %) Manipulator
• Category To Number (< 1 %) ManipulatorStreamable
• Column Resorter (< 1 %) ManipulatorStreamable
• HiLite Row Splitter (< 1 %) Manipulator
• Reference Row Splitter (< 1 %) Manipulator
• Column Splitter (< 1 %) ManipulatorStreamable
• Statistics (< 1 %) Visualizer
• Shape Manager (< 1 %) Visualizer
• Similarity Search (< 1 %) Manipulator
• Math Formula (Multi Column) (< 1 %) ManipulatorStreamable
• Excel Reader (XLS) (< 1 %) SourceStreamableDeprecated
• Molecular Properties (< 1 %) Other
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Best Friends (Outgoing)

• Image Port Writer (13 %) Sink
• HiLite Row Splitter (9 %) Manipulator
• HeatMap (JFreeChart) (9 %) Visualizer
• Expand Well Position (6 %) Manipulator
• Plate Heatmap Viewer (6 %) Visualizer
• Table Writer (6 %) Sink
• Plate Row Converter (4 %) Manipulator
• Normalize Plates (Z-Score) (4 %) Manipulator
• R Plot (4 %) Visualizer
• Image To Table (4 %) Other
• CSV Writer (4 %) SinkStreamable
• GroupBy (4 %) Manipulator
• Conditional Box Plot (4 %) Visualizer
• Normalize Plates (B-Score) (2 %) Manipulator
• Normalize Plates (NPI) (2 %) Manipulator
• Normalize Plates (POC) (2 %) Manipulator
• Z-Primes (PC x NC) (2 %) Manipulator
• Domain Calculator (2 %) Manipulator
• Column Filter (2 %) ManipulatorStreamable
• Filter Apply (2 %) ManipulatorStreamable
• Row Splitter (2 %) ManipulatorStreamable
• Scatter Plot (2 %) Visualizer
• Distance Matrix Calculate (2 %) Manipulator
• Range Splitter (< 1 %) Manipulator
• Dose Response (R) (< 1 %) Learner
• Table to String (< 1 %) Manipulator
• Rule-based Row Filter (< 1 %) ManipulatorStreamable
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Workflows

• 01_Visualization_of_screening_data
• 06_Visualization_of_screening_data_2

Update Site

To use this node in KNIME, install HCS-Tools for KNIME from the following update site: