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Sample attributes view

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Sunburst
Scatterplot
Serial
List
Genetics
Data dictionary

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Customize color:
Note: Saving these filters will replace any other custom sample groups.

Select an attribute for the X axis:

Select an attribute for the Y axis:

Select an attribute:
Note: Serial table is limited to four attributes. Please remove one or more before adding others.

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Patient ID
Timepoint 1
Timepoint 2
Timepoint 3
Timepoint 4
Combine selections across categories with:
Or And

Enter sample or patient IDs separated by commas or line breaks

Enter a name for this group of samples, if desired

Note: Saving this group will replace any sample-based filters set in Sunburst, Serial, or Genetics tabs.

Create a subgroup of samples with genetic traits in common. Start by searching for variants in a gene:
Gene
Note: these search results are affected by global filters

No variant data found.

No additional variants found.

Gene
Start
End
Type
Amino acids
Protein position
Ref
Alt

0 unique samples selected

Enter a name for this group of samples, if desired

Note: Saving this group will replace any sample-based filters set in Sunburst, Serial, or List tabs.

0 samples currently saved as genetic group

0 samples selected

Label for group: Note: Saving this group will replace any sample-based filters set in the Sunburst, List, or Genetics tabs.

Sample data
Patient data
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Filtered sample data Export table
All sample data Export table

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AML Patient Data Export table

Data dictionary

Sunburst panel

Note: this information pertains to the Sunburst panel. To see information for the Serial, Scatterplot, List, or Genetics panels, click the corresponding panel buttons.

This view displays sample attribute data (also referred to as clinical data).

It presents options for defining a global sample-based filter based on sample attributes such as diagnosis and treatment.

A filter set here will affect the data shown in all views that display and/or export sample-based data.

Sample attribute categories are added to this plot as concentric rings, segmented by sample attribute values. Segment size corresponds to the number of samples with that value. As more categories are added they are nested, so the order of addition makes a difference.

Sample attribute categories are color-coded, and the values within that category are varying shades of their category color.

Missing or blank sample attribute values are indicated by a crosshatch pattern.

Drag a sample attribute category from the blue left-hand column into the white right-hand column to add it to the Sunburst plot. You may drag in the opposite direction to remove a category from the plot.

To view the values for a category, click the "+" to the left of the category name to expand its list of values.

Clicking the checkbox next to a value label in the expanded list will highlight the corresponding segment(s) in the plot. This will also filter the "Sample data" table below the plot.

Mousing over a segment in the Sunburst plot will produce text labels in the upper left, reflecting each level of nested categories and values for that particular segment.

Dragging a category out of the white column and back into the blue one will automatically clear any checked boxes, unless they have been saved as a global filter.

To save a subset of samples as a global filter (only "Bone Marrow Aspirate" samples, for example), click the "Save filters" button after selecting the subset. This will affect all views that display and/or export sample-based data, limiting them to only these samples.

A global sample-based filter set here will replace one set in the Serial, List, or Genetics panels.

Scatterplot panel

Note: this information pertains to the Scatterplot panel. To see information for the Sunburst, Serial, List, or Genetics panels, click the corresponding panel buttons.

This view displays sample attribute data (also referred to as clinical data).

Samples appear in this plot as circles, with an x and y position determined by clinical data values.

Select a sample attribute from the X axis drop-down menu and one from the Y axis drop-down menu to view a scatterplot.

Control samples can be omitted by checking the "Omit control samples" checkbox.

Clicking "Swap axes" will tranpose the plot.

Serial panel

Note: this information pertains to the Serial panel. To see information for the Sunburst, Scatterplot, List, or Genetics panels, click the corresponding panel buttons.

This view displays sample attribute data (also referred to as clinical data) sorted by sample date for each patient.

It presents the option of defining a global sample-based filter by hand-selecting samples to be included.

A filter set here will affect the data shown in all views that display and/or export sample-based data.

Data appears in tabular form, with "Timepoints" as columns and patients as rows. Sample attributes are added to the table as color-coded rectangles, with a maximum of four per table cell.

Missing or blank sample attribute values are indicated by a crosshatch pattern.

Select a sample attribute category from the drop-down menu to add it to the table. Colored rectangles will be added to the table, and a legend will appear to the right.

Remove a category from the table by clicking the close button in the legend.

In the legend at right, click the checkbox next to a label to select or deselect all samples with that value at once. Click "hide" to hide values, if desired (and "show" to display them again).

When adding more than one category to the table, you may decide whether to combine selections across categories with "Or" or "And" by clicking those buttons at the top right. Note that within a category, selections will always be combined with "Or." It is only across categories that the combination method can change.

You may select/unselect any individual samples at any time by checking or unchecking the box in the sample's table cell.

Below the table, you will see a count of the total number of samples selected. To save this group of samples as a global filter, enter a label for it, if desired, and click "Save as group." This will affect all views that display and/or export sample-based data, limiting them to only these samples.

A global sample group filter set here will replace one set in the Sunburst, List, or Genetics panels.

Note: this information pertains to the List panel. To see information for the Sunburst, Scatterplot, Serial, or Genetics panels, click the corresponding panel buttons.

No visualizations are displayed in the List panel.

It presents the option of defining a global sample-based filter by entering a list of sample IDs (e.g., "17-00123") to be included.

A filter set here will affect the data shown in all views that display and/or export sample-based data.

Enter a list of sample IDs separated either by commas or line breaks.

To save this list of samples as a global filter, enter a label for it, if desired, and click "Save as group." This will affect all views that display and/or export sample-based data, limiting them to only these samples.

A global sample group filter set here will replace one set in the Sunburst, Serial, or Genetics panels.

Note: this information pertains to the Genetics panel. To see information for the Sunburst, Scatterplot, Serial, or List panels, click the corresponding panel buttons.

The Genetics panel presents the option of defining a global sample filter based on shared genetic traits. A group of samples can be defined by searching by gene(s) and selecting those samples with the desired variant(s).

Global filters affect the results of searching by gene. Any sample-based filters set here and/or variant filters set here determine what variants will be returned.

A filter set here will affect the data shown in all views that display and/or export sample-based data.

Select a gene via the drop-down menu, and any variants found in that gene will be displayed in tabular form.

The table of results can be sorted by any of the blue underlined column headings (Gene, Start, End, Type, Amino acids, Protein position, Ref, and Alt). Click the headings to sort.

Selecting variants from the results will automatically filter samples to match. Variants can be selected via the "Select all" checkbox at the top of the table, or via individual radio buttons on each row. Selecting "or" will include samples with any of the selected variants, whereas selecting "and" will include only samples with all of the selected variants. Selecting "not" will exclude any samples with that variant. Rows with no radio button selected will be ignored.

As you select rows, the total number of unique samples selected will be updated, below the search results table.

The "Sample data" table below the Genetics panel will also be updated with each selection.

Click the "Start over" button above the search results table at right if you want to remove all rows from the table.

To save the samples you have selected as a global sample filter, give the group a name, if desired, and click "Save as group." This will affect all views that display and/or export sample-based data, limiting them to only these samples.

A global sample group filter set here will replace one set in the Sunburst, Serial, or List panels.

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Samples
Genes