Plate Heatmap Viewer

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 (7 %) Deprecated
• Row Filter (6 %) Streamable
• GroupBy (5 %) 
• Join Layout (2 %) 
• CSV Reader (2 %) 
• Concatenate (2 %) Streamable
• String To Number (2 %) StreamableDeprecated
• Column Filter (2 %) Streamable
• Joiner (2 %) 
• Missing Value (2 %) 
• Column Rename (2 %) Streamable
• Math Formula (2 %) Streamable
• Normalize Plates (POC) (2 %) 
• Normalize Plates (Z-Score) (2 %) 
• Plate Heatmap Viewer (2 %) 
• Linear Correlation (2 %) 
• Domain Calculator (2 %) 
• Nominal Value Row Filter (2 %) Streamable
• Row Splitter (2 %) Streamable
• Reference Row Filter (2 %) 
• Sorter (2 %) 
• Normalize Plates (NPI) (1 %) 
• File Reader (1 %) Streamable
• Table Reader (1 %) Streamable
• Java Snippet (1 %) Streamable
• Loop End (1 %) 
• Number To String (1 %) Deprecated
• Column Resorter (1 %) Streamable
• Constant Value Column (1 %) Streamable
• RowID (1 %) Streamable
• String Manipulation (1 %) Streamable
• Rule-based Row Filter (1 %) Streamable
• Color Manager (1 %) 
• Time Domain Features (TDF) (< 1 %) 
• Example Data (< 1 %) 
• Plate Row Converter (< 1 %) 
• Create Well Position (< 1 %) 
• BinningAnalysis (< 1 %) 
• Normalize Plates (B-Score) (< 1 %) 
• Vector Length Normalization (< 1 %) 
• Outlier Removal (< 1 %) 
• CV (< 1 %) Deprecated
• Z-Primes (PC x NC) (< 1 %) 
• Split Collection Column (< 1 %) 
• Loop End (2 ports) (< 1 %) 
• Column List Loop Start (< 1 %) 
• Hierarchical Clustering (DistMatrix) (< 1 %) 
• DBSCAN (< 1 %) 
• Concatenate (Optional in) (< 1 %) Streamable
• Cell Splitter By Position (< 1 %) Streamable
• Column Combiner (< 1 %) Streamable
• Category To Number (< 1 %) Streamable
• Column Merger (< 1 %) Streamable
• Column Rename (Regex) (< 1 %) Streamable
• Column to Grid (< 1 %) 
• HiLite Row Splitter (< 1 %) 
• Reference Row Splitter (< 1 %) 
• Normalizer (< 1 %) 
• Pivoting (< 1 %) 
• Numeric Row Splitter (< 1 %) 
• Set Operator (< 1 %) 
• Column Splitter (< 1 %) Streamable
• Unpivoting (< 1 %) 
• Rule Engine (< 1 %) Streamable
• Statistics (< 1 %) 
• Scatter Plot (local) (< 1 %) 
• Shape Manager (< 1 %) 
• Distance Matrix Calculate (< 1 %) 
• k-Medoids (< 1 %) 
• Similarity Search (< 1 %) 
• Math Formula (Multi Column) (< 1 %) Streamable
• XLS Reader (< 1 %) Deprecated
• Excel Reader (XLS) (< 1 %) StreamableDeprecated
• Excel Reader (XLS) (< 1 %) Streamable
• Java Snippet Row Splitter (< 1 %) Streamable
• Frequency Filter (< 1 %) 
• Bag Of Words Creator (< 1 %) 
• String to Date&Time (< 1 %) Streamable
• Molecular Properties (< 1 %) 
• Fingerprint Similarity (< 1 %) 
• Show all 80 recommendations

Best Friends (Outgoing)

• HiLite Row Splitter (12 %) 
• Normalize Plates (NPI) (7 %) 
• Image Writer (Port) (7 %) 
• HeatMap (JFreeChart) (7 %) 
• Z-Primes (PC x NC) (4 %) 
• Plate Heatmap Viewer (4 %) 
• Linear Correlation (4 %) 
• Row Splitter (4 %) Streamable
• Expand Well Position (3 %) Deprecated
• CV (3 %) Deprecated
• R Plot (3 %) 
• CSV Writer (3 %) Streamable
• Domain Calculator (3 %) 
• Column Filter (3 %) Streamable
• GroupBy (3 %) 
• Scatter Plot (local) (3 %) 
• Plate Row Converter (1 %) 
• Range Splitter (1 %) 
• Dose Response (R) (1 %) 
• Normalize Plates (B-Score) (1 %) 
• Normalize Plates (POC) (1 %) 
• Normalize Plates (Z-Score) (1 %) 
• Table to String (1 %) 
• Image To Table (1 %) 
• Table Writer (1 %) 
• Group Loop Start (1 %) 
• Filter Apply (1 %) Streamable
• Interactive HiLite Collector (1 %) 
• Row Filter (1 %) Streamable
• Column Rename (1 %) Streamable
• String Manipulation (Variable) (1 %) 
• Rule-based Row Filter (1 %) Streamable
• CASE Switch Data (Start) (1 %) 
• Conditional Box Plot (local) (1 %) 
• Molecule Type Cast (1 %) Streamable
• Distance Matrix Calculate (1 %) 
• Image Output (1 %) 
• Show all 37 recommendations

Workflows

• 01_​Visualization_​of_​screening_​data
• 06_​Visualization_​of_​screening_​data_​2
• NucleiClassificationTraining

Installation

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

Developers

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