Plate viewer

What it drawsCopy Anchor Link

An instrument run, on the plate it was actually laid out on.

A real-time or digital PCR instrument reports per well: a position on a plate, a sample, one or more targets, and a fluorescence reading taken once per cycle. This canvas draws that run three ways, and you switch between them without leaving the tab:

• the plate map — every declared well in its true row and column, coloured by what the well holds;
• amplification — raw fluorescence against cycle, every well overlaid;
• melt — raw fluorescence against temperature, every well overlaid.

All three are filtered by the same target picker, so the well you are looking at on the map is the curve you are looking at in the overlay. A file holding more than one run carries a run switcher; each run has its own plate format, its own targets and its own samples.

Beside the drawing the canvas states what the file declares about the run: the RDML version, the experiment and run names, the plate format (rows × columns), how many reactions it holds, how many of those carry amplification points, melting points and a Cq, and the targets and samples by name.

What opens in itCopy Anchor Link

RDML — the open Real-time PCR Data Markup Language, the exchange format instruments and their analysis software export to. Versions 1.0 through 1.4 are read. An RDML file is a zip container, so it is binary on disk; opening one here is what turns it back into a run.

A run with no reactions in it is refused with the reason, not drawn as an empty plate.

What this computesCopy Anchor Link

Almost nothing, and that is the contract: this canvas shows the run as recorded. Cq calling, melt deconvolution, relative quantification (ΔΔCt) and the full digital-PCR analysis belong to the qPCR tool, and a preview here is read-only.

The one quantity computed on this canvas is the concentration of a digital run, because a digital plate has no Cq in any well and would otherwise be an uncoloured plate:

• Cq (quantification cycle) — read from the file, never recomputed. The cycle at which a well's fluorescence crossed the threshold. It is already a logarithm of the starting quantity, so the plate map colours it on a linear ramp.
• Concentration, copies per microlitre — for a partitioned (digital) run, estimated from the fraction of negative partitions by the Poisson relation λ = −ln(negative ÷ total), then divided by the partition volume the file itself declares. The volume is shown in the details beside the plate, as a list where a plate declares more than one, because it is the divisor every concentration on that plate is computed with. A run that declares no partition volume gets no concentration and says so rather than assuming an instrument's nominal value.
• Concentrations from a dilution series span orders of magnitude by construction, so the plate map colours them on a logarithmic ramp and labels it as such.

Uncertainty and qualityCopy Anchor Link

• A well that ran and never crossed the threshold is not a zero. It is drawn uncoloured and counted in the caption, with its reason — reaction ran, instrument recorded no Cq. Painting it at the far end of the ramp would make the emptiest wells the most prominent thing on the plate.
• A fully occupied partition set has no finite concentration. Where every partition is positive, λ is infinite; those wells are left uncoloured and counted rather than clamped to the top of the scale.
• Darker is an earlier Cq on a real-time plate — more starting template. The ramp is reversed for Cq for exactly that reason, and the legend states the direction rather than leaving it to be inferred from the colours.
• The caption states the range the colours span and how many wells are inside it, so a plate whose spread is one cycle cannot be mistaken for one whose spread is fifteen.

ControlsCopy Anchor Link

• View — plate map, amplification or melt. A view the run has no data for is disabled with its reason (this run carries no melting points, so there is no melt curve to draw) rather than offered and then empty.
• Run — which run in the file. Disabled, with its reason, for a single-run file. Switching runs clears the target filter: a target belongs to a run, and carrying one across would draw an empty plate for a target the new run never measured.
• Target — filters all three views at once. Disabled, with its reason, when the run measured a single target.

Every one of these is available in the file-manager preview as well as in the full tab.

Where it appearsCopy Anchor Link

• As a stage tab, opened by clicking the file in the project's file manager, or from the instrument-run picker, which can take an RDML from any project and copy it into the open one.
• As a file-manager preview, drawn by the same component with the same controls, read-only.

The plate map itself is the qPCR tool's own plate map, so the well layout on this canvas and the well layout in the tool cannot disagree about which well is which.

Performance and limitsCopy Anchor Link

• Below 240px wide the canvas refuses to draw. A plate map needs room for the column headers plus twelve cells before two adjacent wells are separable; narrower than that it is a band of colour with no way to tell A1 from A12, which is worse than not drawing it.
• Well values are not printed inside the cells on a large plate — 384 numbers at cell size is noise. The well name leads the tooltip instead, with its value beside it.

ScreenshotsCopy Anchor Link

No composed figure of this canvas exists yet. The pictures on this site are made for the page they sit on rather than captured from a session, and the ones that exist for RDML runs so far were made for the qPCR tool's own pages — the import tab, the curve fits, the digital quantification — not for the plate as a document. Until one is made, the qPCR tool's pages are where a real run is shown.

RelatedCopy Anchor Link

• The qPCR tool is where a run is analysed rather than read: Cq calling, melt analysis, relative quantification and digital-PCR quantification.
• The heatmap canvas draws a matrix that is not a plate.