Create and view a time series graph

You can create and view time series line graphs for Fusions, SNVs/Indels, and CNVs. Fusions time series graphs include Fusion and RNAExonVariant variants, SNVs/Indels graphs include SNV, MNV, and Indel variants, and CNV graphs show CNV variants only. You can customize the Y-axes values and the X-axis labels. Time series graphs can only be created for analyses that were launched with the same analysis workflow.

In the software, you can select one type of variant and generate a single time series graph or you can select multiple types of variants (such as both SNVs and Fusions) and generate multiple graphs simultaneously. If you plot multiple types of variants, the graphs appear side-by-side. You can add or remove variants, or add or remove entire graphs to change the appearance of the graphs in the screen. You can also download image files of time series graphs.

  1. In the Analyses tab, select at least 2 analyses that use the same analysis workflow and contain the data of interest.
  2. Click ActionsTime Series next to Selected Analyses.
    The Time Series screen opens. By default, no filter is applied and all variants from the analyses are displayed. In the Time Series screen, you can view details about the variants and filter the list of variants to find the variants that you want to add to a time series graph.

    The following columns are included in the Time Series table.

    Column

    Description

    Selection box—Use to select the locus in the row that contains the selection box. Select one or more loci to create a chart or charts.

    Locus

    The location of the variant on a specific chromosome or chromosomes.

    Variant ID

    The identifier of the variant.

    Genes

    The affected gene or genes.

    Genotype

    The genotype sequence.

    Type

    The type of variant or call.

    Ref

    The reference sequence.

    Observed Allele

    The observed allele variation.

    Coding

    HGVS notation that represents a nucleotide change.

    Amino Acid Change

    HGVS notation that represents an amino acid change.

    Subtype

    The variant subtype.
  3. (Optional) In the Filter Options dropdown list, select a filter chain from the Filter Chains list to limit variant results.
  4. (Optional) Use the Search field to limit the list of analyses. For example, in the Search field, enter type:FUSION to find fusions. See Searches on the Analysis Results screen for more information.
  5. Select at least one variant in the Time Series screen, then click Generate Chart.

    The order of the variants in the line graph match sequentially with the order in which you select the variants. For example, to show the changes in allele frequency over time from the oldest to most recent, select the oldest time point first, and continue to select variants in sequential order. The first variant that you select is positioned first (in the left-most position of the graph along the X-axis).

    If variants for the analyses are displayed in Locus View, a Select Alleles window opens. For more information, see Locus View versus Allele View of variants.

    1. In the Called Alleles column for each locus, in each dropdown list, select the alleles you want to graph.
    2. Click Select.

    The Chart Preferences window opens.

  6. In the Chart Preferences window, select the X-Axis Label, the Y-Axis Value, and the Variant Label to customize the data displayed in the graph. Available options depend on the analyses.
    Table 1. All Charts

    Label

    Option

    X-Axis Label

    • Analyses Name (default option)

    • Sample Name

    • Sample Collection Date

    • Sample Receipt Date

    • User-defined sample attributes are also available selections if all selected and analyzed samples contain an entry. If any sample included in the selected analyses does not have an entry for the user-defined sample attribute, that attribute is not listed as a chart option.
    Table 2. SNV/Indel

    Label or Value

    Option

    Y-Axis Value

    • Allele Frequency % (default option)

    • Allele Ratio

    • Mol Freq %[1]

    Variant Label

    • Gene + Coding (default option)

    • Gene + AA Change

    • Locus

    • Coding

    • Amino Acid Change

    • Variant ID
    1 Option appears in Ion AmpliSeq™ HD and TagSeq analyses only.
    Table 3. CNV

    Label or Value

    Option

    Y-Axis Value

    • CNV Ratio[2] (default option)

    • Copy Number[3]

    • Ploidy (log scale)

    Variant Label

    • Locus (default option)

    • Genes
    2 Option appears in Ion AmpliSeq™ HD and TagSeq analyses only.
    3 Option appears in Ion AmpliSeq™ analyses only.
    Table 4. Fusions

    Label or Value

    Option

    Y-Axis Value

    • Read Counts Per Million (default option)

    Variant Label

    • Locus (default option)

    • Variant ID

    • Genes
  7. Click Generate.

    The Time Series graph or graphs displayed.

  8. (Optional) Click Download to download a ZIP file that contains PNG files of the graph or graphs.
  9. (Optional) Remove or add the variants that appear in the graph.

    • Click a variant label in the color key at the top of a graph to remove the data points for that variant from the graph. Variants that have been removed from a graph are shaded in the key.

    • Click shaded variant labels in the key to add the data points back to the graph.

    For an example, see Example of dynamic edits to time series graphs.

  10. (Optional) In the table below the graph, deselect current variants or select different variants, then click Generate Chart to add or remove selections from the graphs or create time series graphs with new selections.