geneviewer 0.2.0
New features:
GC_labels(adjustLabels = "spread") puts the gene labels
on one line below the lowest gene, moved apart where they would overlap,
with a line from each label to its gene, as in gene order figures.
leaderLine sets the distance from the genes to the labels
(length) and the style of the lines,
e.g. leaderLine = list(length = 30, stroke = "grey"), or
leaderLine = FALSE for no lines.
spreadPosition = "top" puts the labels above the highest
gene instead. Lines follow labels that are dragged, and start at the top
of the gene when a label is dragged above it, and the labels are spread
again for the genes in view when zoomed in. Themes style the lines too:
they take the lineColor of GC_theme(), can be
set with GC_theme(labels = list(leaderLine = list(...))),
and each built-in theme draws them to match its other lines.GC_zoom() adds a zoom slider below the clusters. Drag a
handle to change the window, drag the window to move it, click the track
to move the window there, and double-click the slider or use the new
reset zoom button of the toolbar to show everything again; the arrow
keys, Home and End work on a focused handle or window. Genes, labels,
links, coordinates and annotations follow the window and are cut off at
the edges of the plot area, and the axis shows the ticks of the window.
mode = "relative" (default) shows the same share of every
cluster, mode = "absolute" the same base pairs;
range sets the window shown first, min the
narrowest window, update = "release" draws only when the
slider is let go, and overview shows the genes of each
cluster in the slider. Saved images leave out the slider and the room it
takes, so they look as if the chart had none. In Shiny,
GC_events(zoom = TRUE) reports the window as
input$<outputId>_zoom on the first render and after
every change, with the base pairs each cluster shows and a
range to pass back to GC_zoom(range = ), and
GC_zoom_to() sets it from the server. Redraws from Shiny
with the same data, range and mode keep the window the user picked; a
new GC_events(render_id = ) marks a new load, which starts
at range again.GC_toolbar() sets the chart’s toolbar: when it shows
("hover", "always" or "never"),
its corner, which buttons it has, the size and colours of its icons and
tooltips, and the icons themselves, by Font Awesome name
(e.g. icons = list(reset = "arrows-to-circle")). Its
tooltips and save menu take a border, corner radius, shadow and font.
Colours, size and the tooltip style can also be set for a theme with
GC_theme(toolbar = list(...)). The built-in themes style
the toolbar to fit: their tooltip style for its tooltips and menu, and
icon colours of the theme (the ECharts toolbox colours for the
ECharts-based themes, muted grey that lights up on dark, black and grey
for print), so the icons stay visible on the dark theme.GC_events(select = TRUE) selects several elements:
Shift-, Ctrl- or Cmd-click adds or removes one, and dragging on empty
space draws a box that selects the elements inside it.
input$<outputId>_selection lists all selected
elements; input$<outputId>_select stays the one
selected last. With drag = TRUE, dragging a selected
element or pressing the arrow keys moves all selected labels, titles,
scales and legend parts together, as one step to undo.GC_events(drag = TRUE) can move legend labels and
markers, each on its own. Save their positions with
GC_element_style("legend", group = ..., part = "label" or
"marker", moveX = ..., moveY = ...). A drag no longer
counts as a click, so dragging a legend item does not hide its
genes.- With
GC_events(drag = TRUE), moves can be undone,
redone and reset: undo, redo and reset icons appear next to the download
icon once something has been moved, and Ctrl/Cmd+Z, Ctrl/Cmd+Shift+Z and
Ctrl+Y work after clicking the chart. Reset moves every element back to
where it was first drawn, keeping positions set with
GC_element_style(), as one step that can be undone. With
select = TRUE, the arrow keys move the selected text or
scale (Shift: 10 pixels). Steps of one element report
input$<outputId>_drag like a drag, with a new
action field ("drag", "nudge",
"undo" or "redo"); steps of more elements
report input$<outputId>_moves once. The download icon
and its formats can now also be used with the keyboard. Drags now move
by whole pixels, also when the chart is scaled.
GC_events(drag = TRUE) can move a whole scale axis or
scale bar from its line, ticks or text. Save per-cluster positions with
GC_element_style("scale", cluster = ..., moveX = ..., moveY = ...)
or the "scaleBar" component.GC_events(rendered = TRUE, render_id = ) reports
successful chart updates through Shiny’s
input$<outputId>_rendered and a bubbling
geneviewer:rendered browser event. The event carries the
update identifier, chart DOM ID (chartId) and widget
dimensions. An omitted render_id generates a unique ID per
update across charts on the page. It fires after drawing and click
setup, and does not fire on resize or failed draws.GC_events() makes a chart report clicks to Shiny:
input$<outputId>_click gives the part of the chart
that was clicked ("genes", "labels",
"scale", "clusterTitle", …), its cluster, and
the row of the clicked gene or link or the legend group, e.g. to show
the details of a gene. highlight = TRUE outlines the part
under the mouse. Charts are not clickable unless it is set. Every part
of the chart is now marked with a data-component attribute
and each cluster with data-cluster, for CSS and
JavaScript.GC_events() can report double-clicks independently of
clicks, enable individual gene and label selection with keyboard access,
and exclude legend clicks from settings handlers. Selection and hidden
legend groups survive redraws and resize for the same data. The payloads
of a gene or label include style, how it is drawn (colours,
opacity, border, shape, text and font), so an editor can show the
current values.GC_element_style() edits or resets one element: a gene,
gene label or coordinate by row ID (and end = "start" or
"end" for a coordinate), so sorting and repeated names do
not redirect an edit, or the title or subtitle of a cluster title,
footer or label by cluster and part. Labels,
titles and subtitles can also change their displayed text, and
coordinates can be hidden. Generated R code can record these calls to
reproduce visual edits. With GC_events(select = TRUE) all
of these elements can be selected one by one.GC_legend(groupStyle = ) styles the legend entry of a
group: its text,
e.g. list(tnsA = list(fontStyle = "italic")) for italic
gene names, and its marker through marker,
e.g. list(A = list(marker = list(stroke = "black"))).GC_transcript(groupStyleExons = , groupStyleIntrons = , groupStyleUTRs = )
style all exons, introns or UTRs of a group, with the options of the
matching itemStyle; style_by sets the column
they are matched against, e.g. style_by = "transcript" to
style one transcript.GC_coordinates(groupStyle = ) styles the coordinates of
the genes of a group: show = FALSE leaves them out,
tick styles their ticks and the other options their text,
e.g. list(other = list(show = FALSE)) to show the
coordinates of the named genes only. style_by sets the
column they are matched against.GC_genes(style_by = ) and
GC_labels(style_by = ) set the column
groupStyle is matched against, to style genes or labels by
another column than the one that sets their colours, e.g. labels by
their text:
GC_labels(label = "name", style_by = "name", groupStyle = list(tnsA = list(fill = "white"))).GC_scale(scale_break_padding = ) also takes the padding
around automatic scale breaks in base pairs, e.g. "500bp",
for the same room around every break; a number is still a percentage. A
gap too short for the padding gets no break.GC_scale(breaks = ) also takes a data frame with
start and end columns and, for breaks per
cluster, a cluster column,
e.g. data.frame(cluster = c("A", "B"), start = c(5000, 8000), end = c(9000, 12000)),
to set different breaks for each cluster in one call.GC_labels(groupStyle = ) styles the labels of all genes
of a group at once,
e.g. groupStyle = list(tnsA = list(fill = "white")) for
white labels on dark genes. The itemStyle of a label takes
precedence over the style of its group.GC_genes(groupStyle = ) styles all genes of a group at
once, with the options of itemStyle,
e.g. groupStyle = list(promoter = list(marker = "box", fill = "grey")).
The itemStyle of a gene takes precedence over the style of
its group.GC_theme() sets the default look of the whole chart:
start from a built-in theme ("default",
"classic", "dark", "vintage" and
"infographic" with the colours of the ECharts default
(version 5), dark, vintage and infographic themes,
"publication" for journal figures, after common journal
figure guidelines (Arial, 7 pt text, black text and axes, italic gene
labels, colour-blind safe colours), or "bw": black and
white with a pattern per group, in the same style), set the font, text
and line colours, background, gene colours and patterns of all
components at once, and change the options of any component
(e.g. labels = list(fontSize = "10px")).
textScale scales all text at once
(e.g. textScale = 1.5), with the title and the default
cluster label width growing with it. Options set with the other
GC_ functions always take precedence over the theme,
whatever the order of the calls. geneviewer_theme() returns
the settings of a built-in theme.GC_pattern() fills genes, exons and legend markers with
a pattern per group, for black and white figures. There are 16 patterns
("diagonal", "dots",
"crosshatch", "checkerboard",
"bricks", "inverseDots" and more). Patterns,
pattern colours and backgrounds can be set per group, and
background = NULL draws the patterns on top of the gene
colours. They are kept in the PNG from the save button.- The save button can now save charts as SVG, with all clusters,
links, legends and titles in one vector file for publications. Hover the
download icon and pick “Save as SVG” or “Save as PNG”.
- Gene colours can be set by the name of a geneviewer palette, besides
the d3 colour schemes:
"okabeIto" (colour-blind safe),
"classic" (clear colours), "vivid" (bright
colours for dark backgrounds), "dark" (soft colours for
dark backgrounds), "vintage" (muted colours),
"infographic" (strong colours), "greys" and
"blues", in GC_theme(palette = ) and the
colorScheme of GC_genes(),
GC_transcript() and GC_color().
geneviewer_palette() returns their colours.
GC_links(label_position = "link") writes the measure of
each link (e.g. its identity) in the middle of the link instead of with
the gene label: only where it fits within its link and clear of the
others, white on dark links. Zoomed in with GC_zoom(),
links widen and more measures are written. Links from data
(e.g. an alignment) can be labelled this way too.GC_cluster(prevent_gene_overlap = "nested") moves only
the genes that lie inside another gene, e.g. an ORF in another reading
frame, to the tracks below; the other genes stay on the first track,
also where they overlap. GC_cluster(overlap_min = ) keeps
genes that overlap by no more than a number of base pairs, or a share of
the shorter gene (e.g. "10%"), on the same track, so genes
that share a base or a stop codon are not split. With
style_by = "geneTrack", GC_genes() and
GC_labels() style the genes and labels of each track,
e.g. groupStyle = list("2" = list(markerHeight = 8)) to
draw the genes of the second track smaller.GC_labels(adjustLabels = "hide") hides labels that
overlap another one instead of turning them; zoomed in, they come back
when there is room.GC_links(colorBarOptions = ) places the color bar:
position puts it in a corner of the plot area
("bottomright", the default, "bottomleft",
"topright" or "topleft") or, with
"legend", in the legend, before the groups or, with
legendSide = "right", after them, lying down in the
legend’s font, as tall as the legend markers and set apart from the
groups; orientation = "horizontal" lays it down as one line
with the title, the lowest measure, the bar and the highest, or with
labels = "below", the title above the bar and ticks below
it, as many as fit. The title of a lying bar is bold. Charts with
inverted links stack the two bars. A bar meant for the legend stands in
the bottom right corner when the chart has no legend. By default the bar
stands bottom right, as before.GC_links(low_color = ) sets the colour of links with
the lowest identity (white by default), e.g. the background colour on a
dark chart.GC_genes(corner_radius = ) rounds the corners of the
“arrow”, “boxarrow” and “box” markers
(e.g. corner_radius = 3 for soft corners; the inner corners
of arrows stay sharp) and sets those of “rbox”. Exons take
cornerRadius in styleExons, and themes in
genes = list(corner_radius = ).
GC_legend(corner_radius = ) rounds the corners of the
legend markers.GC_links(vmin = , vmax = ) set the measures of the
lightest and the full link colour, and the ends of the colour bar (0 and
100 by default): e.g. vmin = floor(min(alignment$identity))
spreads the colours over the identities of an alignment, so differences
are easier to see. Measures outside are drawn in the colour of the
nearest end.GC_legend(align = ) aligns the legend to the left,
centre or right, like GC_title(): "left"
(default), "center" or "right". Each row of a
legend that wraps is aligned on its own, and x moves the
legend from that position. Themes take it in
legend = list(align = ).GC_title(), GC_clusterTitle() and
GC_clusterFooter() now have a documented align
argument ("left", "center" or
"right"), which is checked; it was only taken through
.... The cluster title and footer take one per cluster,
e.g. align = c("left", "right").GC_clusterLabel(align = ) aligns the lines of the
cluster labels to the left, centre (default) or right of their margin,
e.g. align = "left" so the names and the species below them
start at the same place. x moves the labels from that
position.GC_clusterLabel(subtitle = ) adds a second line below
each cluster label, e.g. the species, styled with
subtitleFont (11px and not bold by default).
spacing sets the pixels between the last line of the title
and the subtitle (by default 1.2 times their mean font size), and the
two are centred together on the cluster. Themes colour the subtitle like
the other text, and the dark, vintage and publication themes like their
other subtitles.GC_title(), GC_clusterTitle() and
GC_clusterFooter() now have a documented
spacing argument for the pixels between the title and the
subtitle, which is checked; it was only taken through ....
The cluster title and footer take one per cluster.GC_trackMouse() takes the styles of the coordinate
tooltip (e.g. backgroundColor, fontSize) and
cursor.
Enhancements:
read_fasta() is about 4-5 times faster on large FASTA
files.- Charts are drawn faster and are much smaller in HTML pages, Shiny
apps and R Markdown documents. Gene labels are placed without laying out
the page again for each label, and are only checked against the labels
near them: a cluster of 4,000 labelled genes is drawn about 10 times
faster, also on resize. The gene data is sent to the browser once
instead of twice, and protein sequences (the
translation
and sequence columns) are left out unless an option names
them, e.g. a tooltip formatter with
{translation}, so a chart of the erythromycin BlastP
example is 32 KB instead of 261 KB. They stay in the chart in R, and the
row data of Shiny events no longer includes them unless they are
shown.
protein_blast() is about 3 to 9 times faster and gives
the same results. The aligned sequences are now read from all alignments
at once and identity and similarity are counted for all pairs at once,
so parallel processing is no longer needed: the parallel
argument is ignored and the parallel package is no longer a
dependency.
Changes:
- The documentation of
protein_blast() now describes what
it does: a global (Needleman-Wunsch) pairwise alignment of every protein
pair, not BLASTP. Identity and similarity are counted over the full
alignment, gaps included, so they can be lower than BLASTP values. The
package description cites Needleman and Wunsch (1970) instead of the
BLAST paper, and tooltips of its results say “Best hit” instead of
“BlastP hit with”. The function, its BlastP column and the
erythromycin_BlastP data keep their names.
genbank_to_fasta() now writes to tempdir()
by default instead of next to the input file (use
output_dir = NULL for the old behaviour), and returns the
path of the FASTA file invisibly.- knitr, rmarkdown, tidyr and biomaRt are no longer suggested: they
are only used by the articles of the package website, which are not part
of the package.
- MUMmer is now listed under
SystemRequirements, and the
examples of read_fasta(), read_gff(),
read_bed(), gbk_features_to_df() and
protein_blast() run on example data.
- FASTA and GFF readers now spread metadata with an internal helper
instead of tidyr. Removing the tidyr dependency also avoids its stringr,
stringi and purrr dependencies when they are not required by other
packages, reducing Shinylive startup downloads.
- The padding around automatic scale breaks
(
GC_scale(scale_breaks = TRUE, scale_break_padding = )) is
now a share of the region shown, without the breaks, so all breaks get
the same room around them; long breaks used to get much more padding
than short ones.
- With
GC_scale(axis_type = "range"), scale breaks are
given in the positions of the data, like the annotations and the line,
and move with the genes; they were taken as positions on the shifted
axis.
GC_align() leaves scale breaks out of the shared range:
a cluster with breaks gets a range that much longer, so all clusters
keep the same scale. The padding of the scale and the line is now a
share of the range shown, without its breaks.GC_align() now shifts the clusters instead of
stretching them, so all clusters keep the same scale: genes of the same
length are drawn at the same width, also when the clusters differ in
length. The alignment is kept when GC_scale() is called
afterwards, also with axis_type = "range";
GC_scale() used to undo it.- Cluster footers aligned “left” (the default) or “right” now line up
with the genes and the cluster title: “left” started at the edge of the
chart, in the left margin of the cluster (under a cluster label), and
“right” ended one left margin short of the last gene. Footers that are
not centred move right by the left margin of the cluster (50 pixels by
default); an
x used to line them up with the genes
(e.g. x = 50) can be removed. The examples in the vignettes
are updated.
- Links now fade to nearly white (10% of the link colour) at the
lowest measure instead of white, so they stay visible on the background.
The colour bar now runs from
vmin to vmax (0%
to 100% by default) instead of from the lowest to the highest measure in
the data.
- The title and labels of the link colour bar are now in sans-serif,
like the other text; they used the serif font of the browser.
- With a theme background, the UTRs of transcripts are filled with the
background instead of white.
- White legend markers (e.g. “No Hit” or a white custom colour) now
get a light grey outline, so they stay visible on a white
background.
- A cluster margin set with
GC_grid(margin = ) is now
kept by GC_clusterLabel() without width,
whatever the order of the calls; GC_clusterLabel() called
after GC_grid() set the margin to 100px.
GC_clusterLabel(width = ) still sets the margin.
- Options given as a list (e.g.
labelAdjustmentOptions,
colorBarOptions = list(labelOptions = )) now keep the
defaults of the options they leave out, at every level.
- The geneviewer vignette has a new “Themes” section on
GC_theme(): the built-in themes, the global settings and
palettes, textScale, options per component and making a
theme of your own with geneviewer_theme().
- The “Example charts” article has a new example: the
blaKPC-2 plasmid pQEB1 and four variants, with links that show
inversions and inserted transposons. Its data are in the new datasets
pQEB1_plasmids (genes) and pQEB1_alignment (a
nucmer alignment), made by data-raw/pQEB1_plasmids.R from
the GenBank files.
- New tutorial “Reproducing a published figure: Tn7-like transposons”,
which rebuilds Fig. 3 of Peters et al. (2017) step by step: scale
breaks, lining up on a gene, group styles for genes, labels and the
legend, and saving as SVG. The “Example charts” article shows the
finished chart, which also replaces an example chart in the README. Its
data are in the new dataset
tn7_crispr_elements, made by
data-raw/tn7_crispr_elements.R from the GenBank
records.
- The “Example charts” article has a new example for
GC_zoom(): the genomes of eleven coronaviruses from the
four genera, after Fig. 1 of Chazal (2021) and ordered by subgenus, with
the ORFs that lie inside another gene on a lower track and links between
homologous genes. Its data are in the new dataset
coronavirus_genomes, with the homologous genes of closely
related neighbouring genomes and their protein identity, made by
data-raw/coronavirus_genomes.R from the GenBank
records.
- The “Example charts” article has a new example for
GC_labels(adjustLabels = "spread"): the mitochondrial gene
order of the locust and human, after Fig. 3 of Jameson et al. (2003),
with each circular genome rotated to start at COX1 and the gene labels
on one line below the genes. Its data are in the new dataset
mitochondrial_gene_order, made by
data-raw/mitochondrial_gene_order.R from the RefSeq
records.
Bug fixes:
read_fasta() reads the FASTA headers again with
Biostrings 2.81 and later, which moved them out of the row names of
as.data.frame(); it found no keys and returned no
rows.- Labels turned to avoid overlap
(
GC_labels(adjustLabels = TRUE)) are no longer cut off: a
label that would turn out of its cluster, e.g. above it or past the
right end of the plot area, is now hidden, and comes back when there is
room for it, e.g. when zoomed in.
GC_annotation() draws a text annotation by default, as
documented; its default type was "textAnnotation", which
was not drawn. An unknown type is now an error that lists
the types.GC_transcript() keeps the GC_events() and
GC_toolbar() settings of the chart; they were lost when
they were set before it.- The stylesheet of the chart no longer styles elements outside it:
its rules for the
hovered, label,
legend and gene classes only apply inside a chart.
- Links can be clicked and highlighted with
GC_events():
they are drawn below the SVGs of the clusters, which took every click
over the chart, so a click on a link was never reported. Drawing,
GC_trackMouse() and saved SVG and PNG files are
unchanged.
mummer_alignment() now finds MUMmer on Windows; it
looked for it with a Unix-only shell command and always reported it as
not installed.mummer_alignment() now runs in a unique working
subdirectory, preserving existing input and output files and cleaning up
its own files on success or failure. With
remove_files = FALSE, files are retained in that
subdirectory of output_dir.- Bundled D3 and FileSaver.js now include their upstream license
notices and copyright attribution.
- FASTA tests now skip when the optional Biostrings package is
unavailable.
read_bed() no longer drops records when feature names
contain “track”, and preserves records across multiple track
declarations.get_introns() only adds positive gaps between covered
regions, including when exons and UTRs overlap, nest or are
adjacent.- Tooltips of
protein_blast() results: genes of the query
cluster are shown as “Query gene” instead of a hit with themselves (or
“No Hit”) at 100% identity, and genes without a hit no longer show empty
“Identity: %” and “Similarity: %” lines. In GC_tooltip()
formatters, a line whose fields all have no value is now left out.
GC_links() leaves the chart unchanged when supplied an
empty alignment.- GFF and FASTA metadata named
id no longer collides with
internal record identifiers.
- PNG export now rasterizes the same SVG snapshot as SVG export, so it
works inside apps whose surrounding styles use modern CSS colors such as
oklch(). Backgrounds, patterns and the device pixel ratio
are retained without parsing the app’s stylesheets. The unused
html2canvas dependency is no longer bundled.
- In Shiny, fixed pixel chart widths now size the whole widget before
drawing, so the title, clusters and legend share the requested width
instead of shrinking the clusters into the output container. Switching
back to a responsive chart restores the original output width;
standalone and height sizing are unchanged.
- When
GC_links() is called more than once, the link
labels of each call now use the options of that call
(label, measure, labelStyle,
value1, value2, …); all link sets used those
of the first call. A gene in more than one link set gets one label.
- The
start and end of the line of a cluster
(GC_sequence()) now stay with the genes with
GC_scale(axis_type = "range"), like the annotations,
whether they are set before or after GC_scale(); they were
taken as positions on the shifted axis.
- The line of a cluster now stops at a scale break
(
GC_scale(breaks = ) or scale_breaks = TRUE)
and starts again after it, so the break marks show a real gap; the line
ran on between them.
- A gene made taller or moved with
GC_genes(itemStyle = )
(e.g. markerHeight, arrowheadHeight or
y) no longer moves the labels of the other genes in its
cluster. The labels and track spacing used the size and position of
whichever gene was drawn last.
- Annotations now stay on their genes with
GC_scale(axis_type = "range"): the range axis moves the
genes of each cluster to start at 1, and now moves the annotations of
the cluster (x, x1, x2 and
position) with them, whether they are added before or after
GC_scale(). They used to be drawn too far to the
right.
- A wrapped cluster label (
GC_clusterLabel()) keeps its
<b>, <i> and
<u> styles when the tagged text runs over two lines,
e.g. "pQEB1 <i>E. cloacae ECL-21</i>"; the tags
were shown as text. The lines are now also measured without the tags, so
they no longer break too early.
- The legend of a chart with a fixed width
(e.g.
GC_chart(width = "900px")) no longer gets smaller in
a wider browser window: it was laid out at the width of the window and
then scaled down into the chart, e.g. in a page saved with
htmlwidgets::saveWidget().
- The bottom of letters such as g, y and p in a title without a
subtitle is no longer cut off: the default title height is now 40 pixels
instead of 30, so
GC_title(height = ) is no longer needed
for titles of 16 or 18 pixels.
- A named list of
customColors (in
GC_color(), GC_genes() and
GC_transcript()) that leaves out groups no longer makes
those groups white: they keep the colours of colorScheme,
the theme palette or the default colours,
e.g. GC_color(customColors = list(Other = "grey")) only
changes “Other”. GC_color() now takes
colorScheme together with a named list of
customColors.
GC_transcript() no longer drops the settings of the
whole chart made before it: the title, legend, theme and
GC_grid() margins and direction are kept. Settings per
cluster are for the old clusters and are set after
GC_transcript().GC_legend(backgroundColor = ) now sets the legend
background; it had no effect.- When a chart is redrawn in Shiny, styles of
GC_chart(style = ) that are no longer set are removed;
e.g. a background colour stayed after it was removed.
GC_annotation(type = "symbol") no longer also draws a
curve from x = 0 to x = 100.- The default gene colours now give 30 different colours. Groups 12
and 22, 13 and 26, 15 and 29, and 20 and 25 had the same colour; groups
22, 25, 26 and 29 now get new colours.
- Legend colours now match the gene colours when some genes have an
NA group. Genes with an NA group are now
always white, also with colorScheme or
customColors.
GC_annotation(type = "arrow", arrowStyle = ...) now
applies all arrowStyle options (e.g. stroke,
strokeWidth, fillOpacity) to the arrow head;
only fill was used.- Arrow heads of
GC_annotation(type = "arrow") and
type = "textMarker" no longer take the size and colour of
an arrow at the same position in another cluster or chart.
GC_scale(breaks = ...) now works with breaks in any
order; breaks not sorted by start put genes and axis ticks at the wrong
position.GC_coordinates() no longer stops the chart from drawing
when a cluster has no genes in view (e.g. after
GC_scale(start = , end = )); clusters below it and the
bottom legend were missing.- The tooltip
mouseout handler no longer relies on the
deprecated global window.event.
- Each chart now uses its own
GC_tooltip() options; with
several charts on a page, tooltips took the colours and font of another
chart. Tooltips are now created inside the chart, so redraws (e.g. on
resize) no longer add <style> tags to the page or
(with GC_trackMouse()) extra tooltip elements.
- Clicking a legend item no longer hides genes that were clicked off
in the legend of another chart on the same page.
GC_trackMouse() now shows the right position to the
right of scale breaks (it was too small by the width of the breaks on
the left).- Charts no longer create the global JavaScript variables
to and linearScale, which could overwrite
variables of the same name on the page.
- Gene labels from
GC_labels() and identity labels from
GC_links() no longer share element ids. The overlap check
of a gene label used the identity label with the same id, so identity
labels were rotated instead of the gene labels.
GC_genes() and GC_transcript() no longer
drop the colours from GC_color() and the patterns from
GC_pattern() when called after them. Their
colorScheme and customColors now also set the
legend colours (when no cluster or selection is given), so the legend
matches the genes.- Identity (or similarity) labels from
GC_links() and
gene labels from GC_labels() no longer overlap. Each gene
now has one label with the gene name and, below it, its identity; when
labels are rotated to avoid overlap, both are shown on one line
(e.g. “eryK 64.1%”).
- With
GC_cluster(prevent_gene_overlap = TRUE), labels of
genes on the lower tracks are now drawn below their gene and rotate
downwards when they overlap, instead of above the gene, under (and
rotated into) the genes of the track above. A label stays above its gene
when a gene of the next track is below it and the space above is
free.
itemStyle values of 0 are no longer ignored in
GC_labels(), GC_genes() and
GC_transcript() (e.g. rotate = 0,
y = 0 or cornerRadius = 0 for one gene); they
fell back to the general option.GC_sequence(start = 0) and end = 0 are no
longer ignored; the line started at the first gene instead.GC_sequence(markerStyle = list(gap = )) is now a
distance in pixels between each break marker and the break, the same for
every break. It was a percentage of the marker’s x position, so breaks
further right opened wider. Charts that set gap get a
narrower gap.- A percentage
GC_title(height = ) or
GC_legend(height = ) now follows the chart height when the
chart is resized; it kept the pixel height of the first draw.
- Smaller fixes: legend items fade on hover again (an invalid CSS
selector dropped the transition; it now only animates the opacity, so
rotated gene labels no longer swing into place on every draw), legend
items have unique ids, the 3’ and 5’ transcript labels have their own
classes (
three-prime-label, five-prime-label),
and unused or invalid styles were removed from the footer subtitle and
the link layer.
- The
GC_links() colour bar now shows a gradient for each
link colour on the chart: the inverted gradient only when at least one
link (in any GC_links() set) joins opposite strands, and
the normal gradient only when at least one link joins the same strand.
Charts with only inverted links showed only the normal gradient, and
charts with forward and reverse normal links showed an inverted
gradient. The link data is no longer modified.
GC_chart() no longer errors when height is
a percentage (e.g. height = "100%").GC_cluster(prevent_gene_overlap = TRUE, cluster = ...)
now stacks overlapping genes in the selected clusters instead of the
first ones.read_gbk() no longer creates fake features from wrapped
qualifier lines that start with a feature name (e.g. a
/note line starting with “gene”) or from feature keys that
start with another key (e.g. CDS_motif read as
CDS).read_gbk() now keeps qualifier values intact
(e.g. closing brackets in "... (PPTase)") and no longer
errors on empty values (/pseudo="") or values that contain
/key=.read_bed() no longer adds 1 to chromEnd,
thickEnd and blockSizes (BED ends are already
1-based), matching rtracklayer::import.bed(). Values in
these columns are now 1 lower than before. Block columns are now always
lists, so single-row BED12 files no longer error and files where every
row has the same number of blocks are read correctly.protein_blast() now works when the cluster column has a
name other than "cluster" (set with the
cluster argument).read_gff() now URL-decodes attribute values
(e.g. %2C to ,), keeps values that contain
=, trims spaces around keys, keeps # inside
lines, stops at a ##FASTA section and no longer errors on
rows with empty or missing attributes.read_fasta() now reads files with a single sequence
that has a location, keeps header values with spaces or
square brackets intact
(e.g. [protein=3-oxoacyl-[acyl-carrier-protein] reductase],
OS=Homo sapiens), and uses the full span of
join() locations for start and
end.GC_scale(scale_breaks = TRUE) no longer errors on
clusters with a single gene or with only overlapping genes.GC_scale(axis_type = "range") now shifts genes when
hidden = TRUE, only shifts the selected clusters (a single
selected cluster no longer gets the genes of all clusters), keeps gene
tracks from GC_cluster(prevent_gene_overlap = TRUE), and
passes ... on to the scale options.GC_normalize(custom_gaps = ...) now measures the gap
after a gene from its edges, so genes on the reverse strand get the
right gap, and applies the gap after every gene with the given
name.GC_clusterLabel(cluster = ...) without a
title now labels each selected cluster with its own name
instead of the names of the first clusters.- Arguments with one value per cluster no longer error in
if() checks:
e.g. GC_labels(label = c("a", "b")),
GC_genes(group = ...) and
show = c(TRUE, FALSE) in GC_labels(),
GC_clusterLabel(), GC_clusterTitle(),
GC_clusterFooter(), GC_coordinates(),
GC_scaleBar() and GC_tooltip(). Arguments that
take a single value (GC_title(show),
GC_align(id, id_column),
GC_transcript(type, transcript),
GC_normalize(group)) now give a clear error.
GC_legend() now gives an error for a group
column that is not in the data, and when a legend is shown without any
group. The checks tested labels, which is not an argument
(it found base::labels), so they never ran.- Links no longer take the colour of another link when a link cannot
be drawn. Removed unused link label code that referred to an undefined
identityLabel.
GC_grid(margin = list(top = , bottom = )) now works for
charts with a percentage height (it errored), and the margins stay
inside the chart height on standalone pages.genbank_to_fasta() now converts GenBank files with
several records (one FASTA record per GenBank record); it errored
before.mummer_alignment() no longer deletes unrelated files
whose name contains <cluster1>_<cluster2> when
remove_files = TRUE; it now removes only the files MUMmer
wrote. Cluster files are matched by exact file name (names like
BGC1+2 work), file paths are quoted in the MUMmer commands,
and names with spaces give a clear error.protein_blast(parallel = TRUE) now works on machines
with one core (it tried to start 0 workers) and always stops its worker
processes, also after an error. It uses at most 2 workers when
_R_CHECK_LIMIT_CORES_ is set (as in
R CMD check).read_gbk() no longer adds translation = NA
to every feature without a translation (e.g. gene and
source).- Removed
.DS_Store files from the package and the unused
internal functions cleanList() and
adjust_to_range().
- Several geneviewer charts in one Shiny app (output IDs without a
-, or Shiny modules) no longer draw into each other’s
containers. The widget now uses its full element ID.
- Charts on the same page no longer share settings through global
JavaScript variables (e.g.
save_button of one chart was
used by another chart after a resize).
- Removed deprecated
.data$ use in tidyselect calls
(select(), pivot_wider()), which gave warnings
with tidyselect >= 1.2.0.
geneviewer 0.1.11
Enhancements:
- Fix for setting tooltip and legend to FALSE
- Fix for links displayed behind graph
- Fix for getting proper strand directions in .gbk files
- Fix for passing additional CSS styles
- Add github actions to build Wasm assets for Shinylive
geneviewer 0.1.10
Enhancements:
- Several fixes to comply with CRAN policies.
geneviewer 0.1.9
Enhancements:
- Added tests for all core functions.
- Fix for applying custom colors in GC_color.
- Fix for setting direction in GC_grid.
- Prepared the package for CRAN release
geneviewer 0.1.8
Enhancements:
- Option to display transcripts using the GC_transcripts
function.
geneviewer 0.1.7
Enhancements:
- Option to perform MUMmer alignments.
- Add option to add a color bar.
geneviewer 0.1.6
Enhancements:
- Option to perform BlastP between gene clusters.
- Add option to add links between genes in clusters.
geneviewer 0.1.5
Enhancements:
- Add preset markers for genes: arrow, boxarrow, box, cbox and
rbox.
- Add options to load cluster information from GenBank and FASTA
files.
geneviewer 0.1.4
Enhancements:
- Add option to add gene links.
- Change package name from GCVieweR to geneviewer.
geneviewer 0.1.3
Enhancements:
- Option to align a specified gene across clusters.
geneviewer 0.1.2
Enhancements:
- Options to add text, line, arrow, rectangle, symbol, terminator and
promoter annotations to a GC_chart.
geneviewer 0.1.1
Enhancements:
- Introduced customizable margin settings for charts, clusters,
titles, and legends.
- Added styling options for the containers of charts, clusters,
titles, and legends.
- Implemented a new feature to display clusters side by side.
- Updated and expanded the documentation to reflect new features and
usability improvements.
geneviewer 0.1.0