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Visualization and plotting

A visualization session can be launched from the search results table within the Vault, after Visualization is activated by a CDD administrator. Contact us if you'd like to try Visualization for yourself.

For the best experience, please use the latest version of Chrome browser.

 

Sending search results from Vault to Vision

Chemical Properties

Protocol Data

Scatter Plot

X and Y axes

Color and Size of points

Data point structure details

Data Table

Filters and other controls

Filters

Export plot

Save a molecule collection in CDD Vault

 

Sending search results from Vault to Vision

Since the Vision session draws the input data from CDD Vault, you will need to configure the search results table in the Vault with all of the results you wish to pass to Vision. Here's a refresher on how to customize your report to adjust the data in the results table.

Numerica data, such as aggregate readouts from protocols, as well as chemical properties can be included in a Vision session. At least one numeric data series must be present in the search results in order to launch a Vision session. While you will be able to visualize up to 4 data series at a time in a single scatter plot, there is no limit on the number of data series (or columns of data) that can be passed into Vision.

A maximum of 40,000 molecules (or rows of data) can be passed to the Vision session. If a larger data-set is submitted, you will see a warming message, and the first 40K molecules will be shown.

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Chemical properties

Numeric chemical properties will be passed as is to the Vision session without any modifications. Make sure to select chemical properties under customize your report in the Vault prior to sending the data to Vision.

 

Protocol readout data

The protocol data in Vision is always aggregated at the molecule/protocol level, which is an important distinction from the Vault search results table, where you can display replicate data points per molecule. This means that any results passed from CDD Vault will be averaged across all runs and across batches, to yield a single value per molecule. With a notable exception of end-point readouts in a protocol with conditions, aggregation will be automatically performed by Vision.

Readout type Protocol with conditions Protocol without conditions
Readout marked as condition
  • Not passed to Vision
     N/A

End-point readout

(plain readout definition)

  • Numeric data type: must create a custom aggregation in CDD Vault prior to sending to Vision
  • Text and other data-types not passed to Vision
  • Numeric data type: arithmetic mean by molecule/protocol
  • Text and other data types not passed to Vision
Normalized against controls
  • Must create a custom aggregation in CDD Vault prior to sending to Vision
  • Arithmetic mean by molecule/protocol
Dose-Response calculation
  • Geometric mean of EC50 by molecule/protocol, per each unique condition set
  • Concentration and response values are not passed to Vision
  • Geometric mean of EC50 by molecule/protocol
  • Concentration and response values are not passed to Vision
Custom calculation
  • Arithmetic mean by molecule/protocol
  • Condition sets as defined by the calculation
  • Arithmetic mean by molecule/protocol

 

Example 1: If your search results table in the Vault includes multiple IC50 values per molecule, and the protocol does not have any conditions, you will see a single IC50 geometric average within the Vision session.

Example 2: If the search results table in the Vault includes IC50s under several conditions, you will see a separate IC50 geometric average for each condition.

Example 3: if your search results table in the Vault contains a dose-response set, including concentrations, inhibitions and IC50ss, you will see a single IC50 value per molecule in the Vision session, while concentrations and inhibitions will not be included.

 

 

Navigating the Vision work space

At least one numeric data series must be present in the search results for the "Launch Vision" icon to light up.

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Once you have a set of results loaded on the Explore Data -> Search page, you will see the "Launch Vision" icon prominently in the search results table header.

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The session is launched in a new window with a default view that includes a scatter plot, a data table, and a set of actions and controls.

 For the best experience, please use the latest version of Chrome browser. 

Scatter plot

The most prominent part of the work space is the 4-dimensional scatter plot. Click on the "expand" icon in the top right corner to maximize the plot.

Screen_Shot_2015-05-01_at_4.16.04_PM.png

 

X and Y Axes

By default, the initial plot is a two-dimensional plot of the first two columns of the data table on the X and Y axes, with the same series used for color-coding and the size of the points.

  • Select the data series you wish to plot on the X and Y axes. The plot will adjust dynamically.

Screen_Shot_2015-04-30_at_1.24.13_PM.png

 

Color and Size mapping

  • Click on the Screen_Shot_2015-04-30_at_11.14.38_PM.png icon, or on the color/size legend under the plot, to change the data-series used for color and size mapping of the points.

set-color-size.png

 

  • Select the data-series to be used for color-mapping from the drop-down. Slide the end-points of the color-wheel to adjust the range of colors. The mouse pointer will show the low and high values of the spectrum.

color-mapping_drop-down.pngScreen_Shot_2015-04-30_at_1.40.48_PM.png

  • Select the data-series for point size mapping in ascending or descending order.

size-mapping.png

 

Plot Zoom and point selection

  • Click and drag the mouse over a selection of point to zoom in on that area of the plot. The plot area will resize dynamically, and you will see the number of selected molecules update in the top right corner of the plot, and filter histograms will update to reflect plot selection.
  • Double click in the empty plot area to reset zoom. Also, reset using "Undo" and "Reset" links at the top of the Vision window.

Screen_Shot_2015-04-30_at_1.56.41_PM.pngScreen_Shot_2015-04-30_at_3.04.07_PM.png

 

Data points

Each point on the plot represents data from a single molecule. Recall that protocol data is aggregated per molecule.

  • Molecules that are missing data in the plotted series will be omitted. You will see a warning message below the plot.

Screen_Shot_2015-04-30_at_3.16.31_PM.png

  • Mouse over a data point to see a preview of the molecule structure.

Screen_Shot_2015-04-30_at_3.20.26_PM.png

  • Click on a data point to see detailed data for the molecule. Click outside of the pop-up to close it. Click on the molecule name in the pop-up to go to the complete molecule record in CDD Vault.

Screen_Shot_2015-04-30_at_3.32.30_PM.png

 

 

Data Table

Underneath the scatter plot, you find a dynamic data table containing the molecule structures and all of the numeric data. This table is similar to the search results table in CDD Vault.

  • Click on the "expand" icon to see the full table.

Screen_Shot_2015-04-30_at_4.48.32_PM.png

  • The table dynamically updates to reflect the molecule selection in the scatter-plot. For example, if you zoom in on 13 molecules in the plot, the table will show 13 molecule out of the originally loaded set. Resetting the plot will reset the table.
  • The check-boxes along the molecules let you cherry-pick further. All molecules are selected by default, and when you de-select a molecule, the corresponding point on the scatter-plot is greyed out, and the count is updated.

 

Controls and Actions

Tabs

Along the right side of the work space runs a section with controls and actions. There are 3 tabs in this section.

Screen_Shot_2015-04-30_at_5.12.11_PM.png

  • Filters allow you to select a sub-set of molecules based on filter criteria
  • Plots currently allows you to export the scatter plots. As Vision matures, this section will incorporate additional plot types.
  • Session allows you to save the active Vision session, and to share it with other members of your CDD Vault.

Filters

The default tab is "Filters", with 4 filters pre-loaded at the start of the session.

  • Each filter is a frequency histogram showing the distribution of the data series. The filter scale ranges from minimum to maximum values of the data series. The height of the bar is determined by the relative frequency of values in that interval.
  • Close a filter using the "x" icon in the corner. Add a new filter to the list from the "Add a filter" drop-down.

Screen_Shot_2015-04-30_at_10.21.46_PM.pngScreen_Shot_2015-04-30_at_10.24.28_PM.png

  • Click and drag around a section of the histogram to select the desired range of data. The scatter-plot will dynamically update all of the plotted data-series based on the filter. The filtering parameter may be one of the plotted series, or another data series.  For example, filter out molecules with the logP from 1 to 3 (while displaying protocol data on the scatter plot):

Screen_Shot_2015-04-30_at_9.52.32_PM.png

 

  • Place the cursor over the selection, and move the entire selected frame to a different range. Place the cursor at the edge of the selection, and drag to contract or expand the frame.

Screen_Shot_2015-04-30_at_9.56.17_PM.pngScreen_Shot_2015-04-30_at_10.07.21_PM.png

 

  • Reset filter by double-clicking outside of the histogram, in an unselected area.
  • Filter data by multiple parameters. When you make a selection on a second filter, the filtering is applied to the previously selected sub-set of molecule. For example filtering 100 molecule by logP 1-3 yielded 78 out of 100 total molecules. Adding a molecular weight filter resultw in 40 molecules from the 78 previously selected.

Screen_Shot_2015-04-30_at_10.35.20_PM.png

 

Plots

The plots tab currently contains an export link for the scatter-plot. Future releases of Vision (throughout 2015) will include additional visualization types on the Plots tab, with the ability to configure multiple plots per single Vision session.

  • Export scatter-plot to a PDF file. You have an option to change the default axes labels prior to export: just start typing new text in the fields- this will over-ride the default.

Screen_Shot_2015-04-30_at_10.44.58_PM.pngScreen_Shot_2015-04-30_at_10.49.49_PM.png

 

Session

The session is tab is still under construction. Future releases of Vision (throughout 2015) will include options to save a dynamic session, and to share the session with Vault members.

Save collection

A set of molecules identified during analysis in the Vision session can be sent back to CDD Vault. Click on the Screen_Shot_2015-04-30_at_11.17.34_PM.pngicon to save selected molecules as a collection.

Screen_Shot_2015-04-30_at_11.16.32_PM.png

Screen_Shot_2015-05-01_at_12.38.44_PM.png

 

 

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