Distance Matrix Reader

Read a distance matrix from a given URL. The file (or URL) is plain ASCII file (possibly gzip'ed) of distance or similarity values. The file may either contain the (upper right) triangular distance matrix or the full distance matrix. A detailed description is given below.

Options

URL

Choose input file here. You can also provide an arbitrary URL here (such as http:// or ftp://).

Separator Char

Enter character separating entries in the table (for instance space, comma or semicolon). Consecutive separator characters will result in errors.

Read Row Header

Check this when the file contains row header information (names of rows)

Read Column Header

Check this when the file contains column header information (will skip the first line then). If the "Read Row Header" option is on, the file is supposed to contain a place holder identifier in the upper left corner. That is, it must not immediately start with the first column name but some (ignored) row header column identifier.

File contains full matrix

The file contains all n square values (whereby n represents the row and column count). Values in the diagonal of the matrix are supposed to contain values representing a distance of 0 (potentially after being normalized). If not, the reader will issue a warning.

Matrix is symmetric

Select this if the table contains the full matrix but the matrix is symmetric (i.e. the value at location (m,n) is equal to the value at (n,m)). Selecting this option will reduce the memory footprint since only the lower triangular matrix is read.

File contains triangular matrix

The file contains only the upper triangular matrix, that is, the first line contains the distances to the n - 1 remaining rows, the second line the distances to the n - 2 remaining rows and so on (whereby n is the line count). If the file also contains the diagonal, check the "Contains diagonal" option.

Contains Diagonal

Each row contains the self-distance of the respective row as first element, which is supposed to be 0.0 after normalization (if it is not a warning is printed).

Apply linear transformation

The values in the file should be linearly transformed by a given scale and offset value (whereby the scale operation precedes the offset operation, the new distance value is y = scale * x + offset). If the file contains similarity values, select offset = 1.0 and scale = -1.0.

Output Ports

Output hosting distance matrix. The matrix is encoded in a single column.

Best Friends (Incoming)

• CSV Reader (25 %) 
• CSV Writer (25 %) Streamable
• Rule Engine (25 %) Streamable
• Distance Matrix Writer (25 %) 

Best Friends (Outgoing)

• Numeric Distances (9 %) 
• Distance Matrix Writer (9 %) 
• Distance Matrix to Network (9 %) 
• Hierarchical Clustering (5 %) 
• Hierarchical Clustering (DistMatrix) (5 %) 
• Hierarchical Cluster Assigner (5 %) 
• Hierarchical Cluster View (5 %) 
• MDS (DistMatrix) (5 %) 
• PCA (5 %) Deprecated
• Distance Matrix Pair Extractor (5 %) 
• RowID (5 %) Streamable
• Unpivoting (5 %) 
• Interactive Table (local) (5 %) 
• Mahalanobis Distance (5 %) 
• Distance Matrix Calculate (5 %) 
• k-Medoids (5 %) 
• Similarity Search (5 %) 
• HierarchicalClusterer (3.7) (5 %) 
• Matrix to Network (5 %) 
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Installation

To use this node in KNIME, install KNIME Distance Matrix from the following update site:

A zipped version of the software site can be downloaded here. Read our FAQs to get instructions about how to install nodes from a zipped update site.

Developers

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