Table¶
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class
cogent3.util.table.
Table
(header=None, rows=None, row_order=None, digits=4, space=4, title='', missing_data='', max_width=1e+100, row_ids=None, legend='', column_templates=None, dtype=None, data_frame=None, format='simple')¶ -
appended
(new_column, *tables, **kwargs)¶ Append an arbitrary number of tables to the end of this one. Returns a new table object. Optional keyword arguments to the new tables constructor may be passed.
Parameters: new_column – provide a heading for the new column, each tables title will be placed in it. If value is false, the result is no additional column.
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col_sum
()¶ returns DictArray summed across columns
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count
(callback, columns=None, **kwargs)¶ Returns number of rows for which the provided callback function returns True when passed row data from columns. Row data is a 1D list if more than one column, raw row[col] value otherwise.
Parameters: - columns – the columns whose values determine whether a row is to be included.
- callback – Can be a function, which takes the sub by columns and returns True/False, or a string representing valid python code to be evaluated.
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distinct_values
(column)¶ returns the set of distinct values for the named column(s)
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filtered
(callback, columns=None, **kwargs)¶ Returns a sub-table of rows for which the provided callback function returns True when passed row data from columns. Row data is a 1D list if more than one column, raw row[col] value otherwise.
Parameters: - columns – the columns whose values determine whether a row is to be included.
- callback – Can be a function, which takes the sub by columns and returns True/False, or a string representing valid python code to be evaluated.
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filtered_by_column
(callback, **kwargs)¶ Returns a table with columns identified by callback
Parameters: callback – A function which takes the columns delimited by columns and returns True/False, or a string representing valid python code to be evaluated.
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format
¶ the display format
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format_column
(column_head, format_template)¶ Provide a formatting template for a named column.
Parameters: - column_head – the column label.
- format_template – string formatting template or a function that will handle the formatting.
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get_columns
(columns, **kwargs)¶ Return a Table with just columns
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head
(nrows=5)¶ displays top nrows
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header
¶ returns header value
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items
()¶
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joined
(other_table, columns_self=None, columns_other=None, inner_join=True, **kwargs)¶ returns a new table containing the join of this table and other_table. Default behaviour is the natural inner join. Checks for equality in the specified columns (if provided) or all columns; a combined row is included in the output if all indices match exactly. A combined row contains first the row of this table, and then columns from the other_table that are not key columns (i.e. not specified in columns_other). The order (of self, then other) is preserved. The column headers of the output are made unique by replacing the headers of other_table with <other_table.Title>_<other_table.header>.
Parameters: - other_table – A table object which will be joined with this table. other_table must have a title.
- columns_other (columns_self,) – indices of key columns that will be compared in the join operation. Can be either column index, or a string matching the column header. The order matters, and the dimensions of columns_self and columns_other have to match. A row will be included in the output iff self[row][columns_self[i]]==other_table[row][columns_other[i]] for all i
- inner_join – if False, the outer join of the two tables is returned.
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keys
()¶
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normalized
(by_row=True, denominator_func=None, **kwargs)¶ returns a table with elements expressed as a fraction according to the results from func
Parameters: - by_row – normalisation done by row
- denominator_func – a callback function that takes an array and returns a value to be used as the denominator. Default is sum.
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row_sum
()¶ returns DictArray summed across rows
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set_repr_policy
(head=None, tail=None, random=0)¶ specify policy for repr(self)
Parameters: - head (-) –
- tail (-) –
- random (-) –
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sorted
(columns=None, reverse=None, **kwargs)¶ Returns a new table sorted according to columns order.
If only reverse is provided, that order is used.
Parameters: - columns – column headings, their order determines the sort order.
- reverse –
column headings, these columns will be reverse sorted.
Either can be provided as just a single string, or a series of strings.
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summed
(indices=None, col_sum=True, strict=True, **kwargs)¶ returns the sum of numerical values for column(s)/row(s)
Parameters: - indices – column name(s) or indices or row indices
- col_sum – sums values in the indicated column, the default. If False, returns the row sum.
- strict – if False, ignores cells with non column/row.
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tail
(nrows=5)¶ displays bottom nrows
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to_array
()¶
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to_dataframe
(categories=None)¶ returns pandas DataFrame instance
Parameters: categories – converts these columns to category dtype in the data frame. Note, categories are not ordered.
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to_dict
(flatten=False)¶ returns data as a dict
Parameters: flatten (bool) – returns a 1D dictionary
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to_json
()¶
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to_normalized
(by_row=False, by_column=False)¶ returns a DictArray as frequencies
Parameters: - by_row – rows sum to 1
- by_col – columns sum to 1
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to_plotly
(width=500, font_size=12, layout=None, **kwargs)¶ returns a Plotly Table
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to_rich_dict
()¶
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to_rich_html
(row_cell_func=None, header_cell_func=None, element_formatters=None, merge_identical=False, compact=False)¶ returns just the table html code.
Parameters: - row_cell_func – callback function that formats the row values. Must take the row value and coordinates (row index, column index).
- header_cell_func – callback function that formats the column headings must take the header label value and coordinate
- element_formatters – a dictionary of specific callback funcs for formatting individual html table elements. e.g. {‘table’: lambda x: ‘<table border=”1” class=”docutils”>’}
- merge_identical – cells within a row are merged to one span.
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to_string
(format='', borders=True, sep=None, center=False, **kwargs)¶ Return the table as a formatted string.
Parameters: - format – possible formats are ‘rest’/’rst’, ‘markdown’/’md’, ‘latex’, ‘html’, ‘phylip’, ‘bedgraph’, ‘csv’, ‘tsv’, or ‘simple’ (default).
- sep – A string separator for delineating columns, e.g. ‘,’ or ‘ ‘. Overrides format.
- center – content is centered in the column, default is right justified
- NOTE (If format is bedgraph, assumes that column headers are chrom,) –
- end, value. In that order! (start,) –
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tolist
(columns=None)¶ Returns raw data as a 1D or 2D list of rows from columns. If one column, its a 1D list.
Parameters: columns – if None, all data are returned
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transposed
(new_column_name, select_as_header=None, **kwargs)¶ returns the transposed table.
Parameters: - new_column_name – the existing header will become a column with this name
- select_as_header – current column name containing data to be used as the header. Defaults to the first column.
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with_new_column
(new_column, callback, columns=None, **kwargs)¶ Returns a new table with an additional column, computed using callback.
Parameters: - new_column – new column heading
- columns – the columns whose values determine whether a row is to be included.
- callback – Can be a function, which takes the sub by columns and returns True/False, or a string representing valid python code to be evaluated.
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with_new_header
(old, new, **kwargs)¶ returns a new Table with old header labels replaced by new
Parameters: - old – the old column header(s). Can be a string or series of them.
- new – the new column header(s). Can be a string or series of them.
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write
(filename, mode=None, writer=None, format=None, sep=None, compress=None, **kwargs)¶ Write table to filename in the specified format. If a format is not specified, it attempts to use a filename suffix. Note if a sep argument is provided, unformatted values are written to file in order to preserve numerical accuracy.
Parameters: - mode – file opening mode
- format – Valid formats are those of the to_string method plus pickle. Will try and guess from filename if not specified.
- writer – a function for formatting the data for output.
- sep – a character delimiter for fields.
- compress – if True, gzips the file and appends .gz to the filename (if not already added).
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