Selecting Bioassays in the plot tool.

[Johan Vallon-Christersson]

Suggested enhancements for plot functionality would enable useful plot capability for 1-channel data. It would also provide useful enhancements for plotting 2-channel data.

– For the Scatter plot tab add for each axis a dropdown menu in which a specific Bioassay can be selected. The alternative to select ‘All Bioassays’ should be available at the top of the list. Selecting ‘All Bioassays’ is the equivalent of how the plot tool currently works.
By adding this functionality users can choose to plot ch1 from one Bioassay against ch1 of any other Bioassay.
– Extended functionality for selecting bioassays to plot. Instead of a dropdown menu (or in addition to) have a ‘Select bioassays’ button for each axis. When selected, a list of the bioassays in the bioassay set is displayed as a new window. This list can be filtered as a regular list with filter bars. One or more bioassays can be selected by using the check boxes and/or by selecting ‘add selected’, ‘add current page’, or ‘add all’ similar to when reporters are added to a reporter list. Available columns in the list should include annotations for the bioassays. In this way it will be possible to select a specific bioassay for each axis in the plot. Importantly, it will enable plotting one group of bioassays against another group of bioassays. For instance, a user might choose to create a scatter plot of a group of treated bioassays against a group of control bioassays. Selection is made easy by filtering the list based on annotations.

– For the Filter tab add the dropdown menu in which a specific Bioassay can be selected. The alternative to select ‘All Bioassays’ should be available at the top of the list. Selecting ‘All Bioassays’ is the equivalent of how the plot tool currently works. The extended functionality described for the Scatter plot tab can be applied here as well.

– For the Histogram plot tab:

1. For Y-axis add the radio button Median.
   
2. For Hi-lo add the radio button Box. This will create a box-plot with the box delineating the IQR and whiskers indicating 5th and 95th percentiles.
   
3. For the X-axis add the possibility (for example by selecting a radio button) to have Bioassays on the X-axis.

[Nicklas Nordborg]

This ticket contains too many features. Features that are independent should be divided into separate tickets.

I have some comments:

• As the plot tool is design it can only work with data where both the X and Y value is coming from a single row (which may be joined from another table). Since data for different bioassays always are in different rows it is not possible (with the current design) to do plots like ch1 in one bioassay agains ch1 in another.
• I think more advanced filtering options should be done outside the plot tool. Ie.create a new bioassayset with the desired filter and then use the plot tool with that data.

[Jari Häkkinen]

We need more flexible plot functionality. For that we need discussions and if they happen we will create new tickets that supersedes this ticket.