Methods and systems for visualizing data quality
A method for generating a data visualization is provided. The method includes receiving a plurality of data points related to fluorescent emissions values from a plurality of reaction sites. The fluorescent emission values include information for a first type of dye and a second type of dye. The method further includes displaying a first portion of the plurality of data points related to the first type of dye in a representation of location of the plurality of reaction sites, and displaying a second portion of the plurality of data points related to the second type of dye in the representation. The method further includes displaying the first portion of the plurality of data points in a scatter plot display. The scatter plot shows fluorescent values related to the first dye on the y-axis and fluorescent values related to the second dye on the x-axis. The method includes displaying the second portion of the plurality of data points in the scatter plot display.
1. A computer-implemented method for generating a data visualization for operating a digital polymerase chain reaction (dPCR) system, the method comprising:
receiving fluorescent emission data, obtained by a detector, the fluorescent emission data comprising a plurality of data points corresponding to fluorescence emission from a plurality of reaction sites of a substrate, the fluorescent emission data indicative of presence or absence of amplification product of a dPCR reaction at the plurality of reaction sites;
determining a first set of data points of the plurality of data points is of a first data quality level based on a quality threshold;
determining a second set of data points of the plurality of data points is of a second data quality level based on the quality threshold;
displaying together on a user interface a first data visualization and a second data visualization, wherein:
the first data visualization displays the plurality of data points in a spatial representation of the substrate such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites of the substrate, the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication, and
the second data visualization displays a histogram containing the first and second sets of data points, wherein:
a first axis of the histogram represents fluorescence emission value,
a second axis of the histogram represents a number of reaction sites,
the first set of data points are displayed with the first indication, and
the second set of data points are displayed with the second indication;
adjusting the quality threshold to an adjusted quality threshold; and
changing the first and second data visualizations displayed on the user interface based on the adjusted quality threshold.
2. The method of claim 1 , wherein the first and second indications differ in color.
3. The method of claim 1 , wherein the first data quality level and second data quality level each comprises a range of data quality values.
4. The method of claim 1 , wherein the histogram displays a first peak of the data points corresponding to emission data indicating absence of amplification product and displays a second peak corresponding to emission data indicating presence of amplification product.
5. A digital polymerase chain reaction (dPCR) system, the system comprising:
a memory; and
a processor for:
receiving fluorescent emission data, obtained by a detector, the fluorescent emission data comprising a plurality of data points corresponding to fluorescence emission from a plurality of reaction sites of a substrate, the fluorescent emission data indicative of presence or absence of amplification product of a dPCR reaction at the plurality of reaction sites;
determining a first set of data points of the plurality of data points is of a first data quality level based on a quality threshold;
determining a second set of data points of the plurality of data points is of a second data quality level based on the quality threshold;
displaying together on a user interface a first data visualization and a second data visualization, wherein:
the first data visualization displays the plurality of data points in a spatial representation of the substrate such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites of the substrate, the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication, and
the second data visualization displays a histogram containing the first and second sets of data points, wherein:
a first axis of the histogram represents fluorescence emission value,
a second axis of the histogram represents a number of reaction sites,
the first set of data points are displayed with the first indication, and
the second set of data points are displayed with the second indication;
adjusting the quality threshold to an adjusted quality threshold; and
changing the first and second data visualizations displayed on the user interface based on the adjusted quality threshold.
6. The system of claim 5 , wherein the first and second indications differ in color.
7. The system of claim 5 , wherein the first data quality level and second data quality level each comprises a range of data quality values.
8. The system of claim 5 , wherein the histogram displays a first peak corresponding to emission data indicating absence of amplification product and displays a second peak corresponding to emission data indicating presence of amplification product.
9. A non-transitory computer-readable storage medium encoded with instructions, executable by a processor, for generating a data visualization for a digital polymerase chain reaction (dPCR) system, the instructions including instructions for:
receiving fluorescent emission data, obtained by a detector, the fluorescent emission data comprising a plurality of data points corresponding to fluorescence emission from a plurality of reaction sites of a substrate, the fluorescent emission data indicative of presence or absence of amplification product of a dPCR reaction at the plurality of reaction sites;
determining a first set of data points of the plurality of data points is of a first data quality level based on a quality threshold;
determining a second set of data points of the plurality of data points is of a second data quality level based on the quality threshold;
displaying together on a user interface a first data visualization and a second data visualization, wherein:
the first data visualization displays the plurality of data points in a spatial representation of the substrate such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites of the substrate, the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication, and
the second data visualization displays a histogram containing the first and second sets of data points, wherein:
a first axis of the histogram represents fluorescence emission value,
a second axis of the histogram represents a number of reaction sites,
the first set of data points are displayed with the first indication, and
the second set of data points are displayed with the second indication;
adjusting the quality threshold to an adjusted quality threshold; and
changing the first and second data visualizations displayed on the user interface based on the adjusted quality threshold.
10. The non-transitory computer-readable storage medium of claim 9 , wherein the first and second indications differ in color.
11. The non-transitory computer-readable storage medium of claim 9 , wherein the first data quality level and second data quality level each comprises a range of data quality values.
12. The non-transitory computer-readable storage medium of claim 9 , wherein the histogram displays a first peak corresponding to emission data indicating absence of amplification product and displays a second peak corresponding to emission data indicating presence of amplification product.
13. The method of claim 1 , wherein the reaction sites are spatially disposed in a two-dimensional array.
14. The method of claim 1 , wherein the first and second data quality levels are above the quality threshold and a third set of data points has a third data quality level below the quality threshold, the third set of data points displayed in the first data visualization with a third indication.
15. The system of claim 5 , wherein the first and second data quality levels are above the quality threshold and a third set of data points has a third data quality level below the quality threshold, the third set of data points displayed in the first data visualization with a third indication.
16. The non-transitory computer-readable storage medium of claim 9 , wherein the first and second data quality levels are above the quality threshold and a third set of data points has a third data quality level below the quality threshold, the third set of data points displayed in the first data visualization with a third indication.
17. The method of claim 1 ,
wherein:
the plurality of data points correspond to fluorescence emission from a first fluorescent dye and a second fluorescent dye,
the first and second sets of data points correspond to fluorescence emission from the first fluorescent dye, and
a third and fourth set of data points of the plurality of data points correspond to fluorescence emission from the second fluorescent dye; and
the method further comprising:
determining the third set of data points by determining the third set of data points is of the first data quality level based on the quality threshold,
determining the fourth set of data points by determining the fourth set of data points is of the second data quality level based on the quality threshold,
displaying together on the user interface with the first and second data visualization a third data visualization wherein:
the first data visualization displays the third set of data points with the first indication and the fourth set of data points with the second indication, and
the third data visualization displays a second histogram, the histogram being a first histogram, the second histogram containing the third and fourth sets of data points, wherein:
a first axis of the second histogram represents fluorescence emission value,
a second axis of the second histogram represents a number of reaction sites,
the third set of data points is displayed with the first indication, and
the fourth set of data points is displayed with the second indication, and
changing the second histogram displayed on the user interface based on the adjusted quality threshold.
18. The method of claim 17 , wherein the first and second data quality levels are above the quality threshold and a fifth set of data points has a third data quality level below the quality threshold, the fifth set of data points displayed in the first visualization with a third indication.
19. The method of claim 17 , wherein the first fluorescent dye is FAM and the second fluorescent dye is VIC.