Select a local file from your computer containing a table of data (tab delimited). The
first column of that file must contain names (or Pathway Tools unique identifiers)
of genes, proteins, reactions,
compounds, or a mix of these. The following column(s) of that
file typically contains experimental numerical values.
The numerical values in the data file might be considered absolute
or relative. If you select absolute,
all negative values in your data file will be skipped.
Furthermore, relative allows you to specify ratios
of columns whereas absolute does not.
The numerical data in your file might need to be interpreted by
the ratio of columns. If this is the case, select "Ratio of two data columns".
Then specify the denominator data column(s).
- 0-centered scale: implies that the numerical data of your file
can contain positive and negative values. The value 0 is considered
to be the center of the numerical values provided in your data file.
Data in log ratio format are 0-centered.
- 1-centered scale: implies that any negative or zero values in your data file
should be skipped. Moreover, the data is centered around the value 1. For example, the value 0.1 is considered to
be at the same distance to 1 as the value 10. So, a logarithm of base 10
is applied to your data before the linear coloring mapping is applied.
If you wish
to include a denominator column for a ratio calculation, you can enter either
a single column number (in which case the same data column will be used as the
denominator for all timepoints), or one column number for each numerator
column number.
The first column of your data file must contain names or identifiers, and not numerical data.
Using this selector you specify what the names are.
Data values are divided into color bins, with the highest value bins
displayed in red, the lowest value bins displayed in green or yellow, and the
middle bins displayed in blue. Three color scheme options are available.
- By default, the color bins range over the entire spectrum, and the cutoff values for the color
bins are derived from the data itself. This means that different experiments
could be displayed using different color schemes, making it difficult to
directly compare them.
- Alternatively, you may specify a value for the maximum
value cutoff bin. All displays that use the same maximum value cutoff will use
the same color scheme (assuming other settings, such as relative vs absolute,
or log format vs non-log format are the same), and are therefore directly
comparable. The maximum cutoff value should be a number, e.g.
2 or 10, etc. All data values greater than the maximum cutoff value will
be displayed in red.
- The third alternative is to use only three color bins: red for data
values that exceed some threshold, yellow for data values less than the
inverse of that threshold, and blue for values in between. The threshold
value should be a number, e.g. 2 or 10.
For a single experiment time step: enter a single column number in the box.
This column corresponds to the data to use from the data file.
For a time series or multiple conditions:
enter a list of column numbers (each column number corresponding
to a single timepoint), separated by spaces, a range of integers (e.g., 2-4), or both.
Important note: The first column of your file contains names and/or identifiers and is column number 0.
The first potential numerical data column is column number 1.
hide
show operations