diff --git a/docs/index.md b/docs/index.md index b01a405..dd776fd 100644 --- a/docs/index.md +++ b/docs/index.md @@ -349,23 +349,52 @@ stack. A phylogeny is a track and so are its sample traits. A circular chromosome and a world map are containers of their own, because a sequence with no ends cannot be drawn as a line without inventing one. +
+ + A read pileup with mismatches, insertions, deletions and spliced alignments + ReadsPileups and single molecules + + + A chromosome ideogram with its bands and a highlighted region + AnnotationIdeograms, genes and coordinates + + + Association statistics above a genotype matrix + VariationAssociation scans and genotypes + + + A dotplot with synteny ribbons between two genomes + ComparisonsDotplots, synteny and alignments + + + The same phylogeny drawn rectangular, circular and unrooted + PhylogenyThree projections of one tree + + + Methylation calls across the origin of replication + SignalCoverage, methylation and squiggles + + + A circular chromosome with its rings + CircularSequences with no ends + + + Cases drawn on a world map beside a phylogeny + MapsWhere the samples came from + +
+
- Thirty-six track types, twenty-two panels, one sheet + All thirty-six on one sheet A gallery of genomic plots on one sheet of twenty-two panels in three columns: a genomic stack, a read pileup, sequence logos, association statistics with a genotype matrix, a dotplot and synteny ribbons, a multiple sequence alignment, variable sites with a phylogeny, a tree, windowed statistics read against a baseline, a circular chromosome, raw nanopore signal, one locus compared across three genomes, Dam methylation across the E. coli origin of replication, an association scan across a whole draft assembly, structural variants as arcs between their breakpoints, the six reading frames, two trees face to face, a human imprinting control region read one molecule at a time, a coding sequence ruled in codons, one molecule aligned in three pieces, SARS-CoV-2 lineage deletions painted onto a phylogeny, and transcription units from start site to terminator
-Twenty-eight of the thirty-six are reachable from the command line. Twenty-seven -of those have a file to read; the twenty-eighth is the coordinate ruler, which -needs none. Trees drawn with metadata, maps and the selection views are -library only. Where the library ends and the command begins is worth saying out -loud, because it is the boundary readers walk into. - -The count is thirty-six because three were removed. Every track has to answer -one question, *does drawing it read the shared scale*, and three that could not -were taken out rather than kept for the sake of a longer list. +Twenty-eight of the thirty-six are reachable from the command line; the rest are +library only, which is a boundary worth saying out loud because it is the one +readers walk into. The count is thirty-six because three were removed: every +track has to answer *does drawing it read the shared scale*, and three that +could not were taken out rather than kept for the sake of a longer list. [Extending](how-it-works/extending.md) has that test and what a new track owes. -A library that says what it threw out is easier to believe than one that says -how much it has. @@ -377,12 +406,59 @@ Several tracks encode a claim rather than a picture, and what they do when the data does not support the claim is what makes them worth having. The refusals are the interesting part. - +
+ +
+ +### A tanglegram is two trees + +

a tanglegram track is drawn from two files, and --against names the second

+ +Handed one file it would draw the tree against itself, which has no crossings, +and no crossings is what a perfect result looks like. The two other tracks that +take a second file are refused the same way. + +
+ +
+ +### A join that matched nothing + +

names the first gene that found no match

+ +A homology join with no hits would outline every gene in every genome as having +no counterpart, which reads as a discovery. The names in a search result and the +names in an annotation are routinely not the same strings, so it says which one +it looked for. + +
+ +
+ +### A scale it cannot infer + +

--identity says whether a column is a percentage or a fraction

+ +Left out it is worked out from the values, and a file whose values are all at or +below one could be either. Read the wrong way round, every ribbon in the figure +becomes a perfect match and nothing fails, so it is refused by name rather than +guessed at. + +
+ +
+ +### Nought reads is not nought per cent + +

skipped, and counted

+ +`modkit` writes a row for a position it could not call, with nought in every +count. Passed through, that is a mark on the baseline saying the cytosine is +unmodified, which is a measurement. The position was not measured. + +
+ +
All four are the same bug, and it has a name here: **a value given for the absence of a value**. It is the class this crate is written against, and it is @@ -532,10 +608,14 @@ when a figure leans on them. [Citation](about/citation.md) has the whole list, the specifications behind -every format the readers take included. Written by **Paula Ruiz-Rodriguez** and -**Mireia Coscolla**, I²SysBio, University of Valencia-CSIC, FISABIO Joint -Research Unit Infection and Public Health, Valencia, Spain. Released under -[MIT](https://github.com/PathoGenOmics-Lab/karyon/blob/main/LICENSE). +every format the readers take included. + +
+ +Built at I²SysBio, University of Valencia-CSIC, and the FISABIO Joint Research +Unit Infection and Public Health, Valencia, Spain. + +
diff --git a/docs/stylesheets/landing.css b/docs/stylesheets/landing.css index 1e3bd6b..86884c8 100644 --- a/docs/stylesheets/landing.css +++ b/docs/stylesheets/landing.css @@ -32,6 +32,11 @@ .md-content__inner:has(.k-hero) { max-width: 62rem; margin-inline: auto; + /* A floor under the gutter. `margin-inline: auto` wins over Material's own + side margin and resolves to nothing on a narrow screen, so without this + every paragraph, heading and card on the page sat flush against both + bezels of a phone. */ + padding-inline: 0.8rem; } /* ------------------------------------------------------------------------- @@ -536,13 +541,15 @@ The refusals and the shelf ------------------------------------------------------------------------- */ -.md-typeset .k-refusal-list { - padding-left: 1.1rem; -} - -.md-typeset .k-refusal-list > li { - margin-bottom: 0.6rem; - line-height: 1.65; +/* The four refusals were a bulleted list of dense paragraphs directly under a + section built out of blocks, which made the page look as though it had given + up halfway down. They are the same kind of thing as the pieces above them, so + they are set the same way. */ +.md-typeset .k-refusals-grid .k-claim code { + font-size: 0.72rem; + background: none; + padding: 0; + color: inherit; } .md-typeset .k-shelf { @@ -607,6 +614,30 @@ line-height: 1.55; } +/* The page used to end by running out: the last thing on it was one paragraph + with the citation link, the authors, two institutions and the licence run + together. A closing block is not more of the page, it is the page saying it + has finished. It carries only what the footer underneath does not, which is + where the work was done: the footer already gives the authors and the + licence, and saying either of them twice two lines apart is worse than not + closing the page at all. */ +.md-typeset .k-colophon { + margin: 2rem 0 0; + padding-top: 1.1rem; + border-top: 1px solid var(--md-default-fg-color--lighter); +} + +.md-typeset .k-colophon p { + margin: 0 0 0.35rem; + color: var(--md-default-fg-color--light); + font-size: 0.72rem; + line-height: 1.6; +} + +.md-typeset .k-colophon p:last-child { + margin-bottom: 0; +} + /* ------------------------------------------------------------------------- Narrow pages ------------------------------------------------------------------------- */