Distance Matrix Reader
KNIME Distance Matrix Extension version 4.3.0.v202011191420 by KNIME AG, Zurich, Switzerland
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
Best Friends (Incoming)
CSV Writer(39 %) StreamableDeprecated- Distance Matrix Writer (19 %)
Table Row To Variable Loop Start(10 %) DeprecatedCSV Reader(6 %) Deprecated- Rule Engine (3 %) Streamable
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Best Friends (Outgoing)
- Statistics (14 %)
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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.
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