Pairwise distance grid
Every barcode against every other as a heatmap, so a cluster of confusable members is a visible block rather than a row in a table.
What it does
The grid draws the full distance matrix of the set under the active metric: one row and one column per barcode, each cell coloured by how far apart that pair is. Dark cells are close pairs.
Where the two histograms tell you how many close pairs exist and which barcodes are involved, the grid shows the structure — whether the close pairs are scattered, or whether five barcodes are all close to each other and form a block. That distinction decides the fix: scattered pairs are edited one at a time, a block means a whole family was generated from too small a seed and should be replaced.
Clicking a cell sends that pair to the set browser, so the grid is also a way of picking a pair out of the picture and looking at it properly.
When you'd use this
- When the nearest-neighbour histogram has a fat left bar and you want to know whether those barcodes are close to each other or to scattered partners.
- On a set built by extending an existing one, where the new members can be well separated from the old and crowded among themselves.
- When a demultiplexing run produced ambiguous assignments and you want to see the neighbourhood that produced them.
- On a small set, as the primary view. Below about a dozen barcodes the grid is easier to read than either histogram.
What this computes
- The full pairwise distance matrix over the set under the active metric — one of the four DNABarcodes metrics (Buschmann, Bioinformatics 33(6)–922, 2017), checked against that package byte for byte — with the distance printed on every cell
- A sequential colour scale domained to the set's own minimum and maximum, not to a fixed range, so the picture shows contrast within this set. Two grids of two different sets are therefore not comparable by colour: read the numbers on the cells when comparing
- The diagonal drawn rather than blanked — zero by construction, kept so rows and columns stay aligned to their labels
The limit is stated, never silently applied. At most 32 barcodes are gridded at once; above that the plot draws the first 32 and prints how many there are in total and how to choose which ones. A truncated matrix that did not say it was truncated would be the worst possible output here, because it looks exactly like a clean one.
Where it lives
The Analysis tab of the Barcode & Index Design panel, and it is detachable — as a floating surface it gets the space a matrix actually needs, which is the reason the detach affordance exists.
Inputs and outputs
In: the working set, or — if you have selected more than one row in the set browser — exactly your selection. That is the mechanism for gridding a subset rather than the whole set.
Out: the coloured matrix, with distances on the cells, over a scale running from the set's minimum to its maximum distance. Clicking a cell focuses that pair in the set browser.
The limit is stated, never silently applied. At most 32 barcodes are gridded at once. Above that the plot draws the first 32 and prints a note saying how many there are in total and how to choose which ones — select up to 32 rows in the set browser and the grid follows the selection. A truncated matrix that did not say it was truncated would be the worst possible output here, because it looks exactly like a clean one.
Controls
| Control | What it changes |
|---|---|
| Metric (panel-level) | Which distance definition the cells report. |
| Selection in the set browser | Selecting two or more rows makes the grid show exactly those, which is how you grid a subset of a large set. |
| Click a cell | Sends that pair to the set browser, labelled with both barcodes. |
| Detach | Floats the grid, where it has room. |
The science
The matrix is the same pairwise computation the rest of the Analyse tab is built on — the four DNABarcodes metrics (Buschmann, Bioinformatics 33(6)
–922, 2017), checked against that package byte for byte.The colour scale is sequential, and it is domained to the set's own minimum and maximum rather than to a fixed range. That means the picture rescales when you change the set: it shows contrast within this set, and two grids of two different sets are not directly comparable by colour. Read the numbers on the cells when comparing.
The diagonal is each barcode against itself and is therefore zero by construction; it is drawn rather than blanked so the rows and columns stay aligned to their labels.
Limitations
- 32 rows. It is a readability limit, not a compute one: 32 labelled rows is roughly what stays legible in a rail-width panel, and beyond it the cells are too small to click reliably. Use the selection to choose which 32.
- Colour is relative to the set, as above.
- It is symmetric and says so nothing about direction — every metric here is symmetric, so the upper and lower triangles carry the same information.
Related
In this group: Edit annotation · Enzyme · Insert sequence · Merge features · Manage enzymes · Dot plot · Dot plot grid · Melt curve · Amplification curves · Population genetics · RNA-seq · Site avoidance heat map · Protein coverage · Reference-gene stability · Digital PCR · Codon usage matrix · Pairwise distance distribution · Nearest-neighbor distances · GC content distribution · Base composition per cycle · Per-cycle channel occupancy · Grammar assembly plan · Gibson assembly plan · Assembly plan build order · Golden Gate assembly plan · Guide track · Primer binding track · Hydropathy profile · Charge vs pH · Amino-acid composition · Hydrophobic moment · Optimization profiles · Digest gel · Virtual gel · Initiation-window fold · Antibody domain map · Electropherogram · Circuit netlist · Circuit transfer functions · Circuit construct · Construction graph · Protocol · Read Quality Profile · Read Alignment · Raw Signal · Verify vs Reference · Chromosomal microarray · Variant calls · Small molecule
Base composition per cycle
What fraction of the pool reads A, C, G and T at each index cycle, with the Shannon entropy of every cycle beneath it.
Per-cycle channel occupancy
What fraction of the pool lights each imaging channel at each index cycle, for the chemistry of the instrument you picked — the check that catches a dark cycle before the run is paid for.