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Update to v1.2.5 #153

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merged 163 commits into from
Sep 27, 2023
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c78185b
Fix error in reoptimized-merge
shwilks Mar 16, 2022
081fc60
`logtiterTableLayers()` function exported
shwilks Mar 16, 2022
5b7e6f9
Fix error when blobs are smaller than grid-spacing used to calculate …
shwilks Mar 16, 2022
a3185cb
* Add the `blobsize()` function for calculating the area/volume of un…
shwilks Mar 17, 2022
96c9521
Correct news
shwilks Mar 17, 2022
ab7eb03
Correct docs for deprecated functions
shwilks Mar 18, 2022
5693dee
Link to deprecated_functions
shwilks Mar 18, 2022
09c46f0
Fix error where serum column base label would remain after turning ti…
shwilks Apr 19, 2022
7eafb24
Set default margins of 0.5 inches when plotting a map
shwilks Apr 21, 2022
23e0e97
Changes and additions to js api
shwilks Apr 25, 2022
1844df7
Add support for insertions in amino acids sequences
shwilks Apr 25, 2022
df1634b
Deal with missing blobs
shwilks May 13, 2022
d68d8cc
Add option to specify a subset of antigens and sera for which to calc…
shwilks May 19, 2022
ef067f4
Update tests
shwilks May 28, 2022
12c0b79
Add method for plotting a map using ggplot i.e. `ggplot(map)`, also s…
shwilks May 28, 2022
62748a2
When coloring by sequence use a more distinct color pallette
shwilks May 28, 2022
0d79588
Add row and column names to sequence matrices
shwilks May 28, 2022
49bc70e
slight code refactoring
shwilks May 28, 2022
eb69840
Update warning message
shwilks May 28, 2022
d59adf3
Add text aesthetic
shwilks May 28, 2022
8e9b3b2
Remove unwanted save reference
shwilks May 30, 2022
a7a4d22
Update docs and imports
shwilks May 30, 2022
4ef2e36
Remove outlier arrow col from documentation
shwilks May 30, 2022
ab658ac
Return stress as part of ac_bootstrap_map
shwilks May 31, 2022
72841af
Add outline width and alpha parameters
shwilks May 31, 2022
8d2c446
Ignore .code-workspace files
shwilks May 31, 2022
5b3ffd1
Ignore .code-workspace
shwilks May 31, 2022
51f1df1
Add ability to plot procrustes lines
shwilks Jun 8, 2022
1d6ac8b
Move r3js from remotes
shwilks Jun 14, 2022
7fd8802
Add options to control arrow appearance
shwilks Jun 14, 2022
5f0451d
Correct indentation
shwilks Jun 14, 2022
d5c5d8b
Correct triangles
shwilks Jun 14, 2022
9c94bac
Update date and dependencies
shwilks Jun 14, 2022
2e07307
Tidy up imports and dependencies
shwilks Jun 14, 2022
f1d8055
Update documentation
shwilks Jun 14, 2022
a4040b9
Remove unnecessary curly braces in documentation
shwilks Jun 14, 2022
c5c2a41
Make description title case
shwilks Jun 14, 2022
aabd872
Remove trailing whitespace
shwilks Jun 16, 2022
0869641
Add new binary build for v1.1.38
shwilks Jun 22, 2022
2770b24
Do not use `\(` syntax
shwilks Jun 23, 2022
42a743a
Correct error when plotting cases where blobs were calculated for onl…
shwilks Aug 10, 2022
969655c
Only show plot outlier arrowheads if point is marked as shown
shwilks Aug 10, 2022
d2c00eb
Numeric table distances account for dilution stepsize setting of map
shwilks Aug 10, 2022
9f96c26
Increment to 1.1.39
shwilks Aug 10, 2022
15d79df
Return more helpful error message
shwilks Oct 28, 2022
9fd1720
Run pkgdown on mac
shwilks Nov 17, 2022
b08f180
Allow for missing match cases
shwilks Nov 17, 2022
8cca419
Deal with cases where legend groups do not contain any members
shwilks Nov 17, 2022
9e56aa3
Update r3js lib
shwilks Nov 17, 2022
5285421
Set dilution stepsize when calculating numeric_min_tabledists
shwilks Nov 17, 2022
1c19199
Correct segments argument for new r3js library
shwilks Nov 17, 2022
6431ffa
Add hack to resize points
shwilks Nov 17, 2022
6a1f5ec
Correct shape descriptions for new r3js library
shwilks Nov 17, 2022
e49d949
consolidate testdata path
shwilks Nov 17, 2022
07f7352
Add some options to view.acmap to set the starting viewer translation…
shwilks Nov 17, 2022
d48e190
Add option to copy viewer rotation etc. settings
shwilks Nov 17, 2022
9e0b390
Try and fix gl point size problem
shwilks Nov 17, 2022
0b2eb75
minor edits
shwilks Nov 17, 2022
b96b1e1
Update to v1.1.40
shwilks Nov 17, 2022
d3904e9
Update line segments argument
shwilks Nov 28, 2022
ac6f12a
Correct line segments argument
shwilks Nov 28, 2022
697fd05
Fix the implementation of glarrow
shwilks Dec 21, 2022
f45e36f
Update documentation
shwilks Dec 21, 2022
d73cce0
Descrease number of external packages required
shwilks Dec 21, 2022
c52cdd4
Remove unneccessary files
shwilks Dec 21, 2022
5765fd1
Update description
shwilks Dec 22, 2022
c83daad
Update R-CMD-check
shwilks Dec 22, 2022
8bde4c8
Update pkgdown action
shwilks Dec 22, 2022
4828ac6
Remove usage of sprintf
shwilks Dec 23, 2022
e95199f
Use linewidth instead of size
shwilks Dec 23, 2022
cdc5742
Remove map diagnostics vignette
shwilks Dec 23, 2022
570f637
Require ggplot >= v3
shwilks Dec 23, 2022
5f20137
Use .data keyword
shwilks Dec 23, 2022
0cd09d1
Use .data keyword
shwilks Dec 23, 2022
91413fd
set seed
shwilks Dec 23, 2022
207b309
Import .data from ggplot2
shwilks Dec 23, 2022
2c0c43f
Update fortran compiler installation instructions
shwilks Dec 23, 2022
588b1bf
Change setup file
shwilks Dec 28, 2022
595ab62
Reduce size of hemisphering arrows
shwilks Dec 29, 2022
afb5a15
Correct maxpointsize for pixel ratio size
shwilks Dec 29, 2022
5861e59
Remove duplicated shader code
shwilks Dec 29, 2022
c2ac2ae
Change arrow linewidth depending on the number of dimensions
shwilks Dec 29, 2022
9278fd8
Correct sequence change information
shwilks Dec 29, 2022
f8b98f5
Do not export test viewers by default
shwilks Dec 29, 2022
ac32b9d
Update .gitignore
shwilks Jan 3, 2023
28503fe
Remove previous builds
shwilks Jan 3, 2023
b6d4c95
Remove .afdesign file
shwilks Jan 3, 2023
636d8b4
Decrease image sizes
shwilks Jan 3, 2023
53eb9f0
Return null array for NA points
shwilks Jan 31, 2023
2dd16a7
Correct argument for updated r3js library
shwilks Jan 31, 2023
656744b
Remove legend for outline width when doing ggplot.acmap
shwilks Jan 31, 2023
1355ac6
Deal with missing blob cases
shwilks Jan 31, 2023
e2248a8
Increase size of boostrap point blobs in 2D
shwilks Jan 31, 2023
b599385
Correct hemisphering error and add test
shwilks Jan 31, 2023
d2d09fb
Remove unnecessary readme breaks
shwilks Feb 6, 2023
cd166ed
Correct typo
shwilks Feb 6, 2023
884ee8d
Update roxygen version
shwilks Feb 24, 2023
bb47e93
Add `grid.lwd` option to control grid linewidth in `ggplot(map)`
shwilks Feb 24, 2023
6446388
Add antigen and sera names to vector when retreiving antigen and sera…
shwilks Feb 24, 2023
3bcbdd4
Add new options and default methods to use when merging titers as des…
Apr 24, 2023
83aecc1
Return a more useful error if `bootstrapBlobs()` is run on a map wher…
Apr 24, 2023
41049e6
Add `grid.margin.lwd` option to control grid margin linewidth in `ggp…
Apr 24, 2023
6cf6e13
Add internal function to lower point drawing order in a map plot
Apr 24, 2023
5604160
Ignore .vscode
Apr 24, 2023
5fdd870
Ignore .vscode
Apr 24, 2023
98c1440
Update docs
Apr 24, 2023
3fbc080
Improve user interruption of map optimization runs
Apr 24, 2023
f2a7b47
Add test for bootstrap map with no bootstrapping done
Apr 24, 2023
d84c82a
Account for the fact that the vectors are named
Apr 24, 2023
7c647f9
Add titer tables
Apr 24, 2023
a890d3c
Account for warning
Apr 24, 2023
f92a8aa
Update docs
Apr 24, 2023
849ef3b
Update version
Apr 24, 2023
12ab217
Make headings consistent
Apr 25, 2023
6d26ebd
Remove unnecessary Racmacs:::
Apr 25, 2023
dc5fadd
Titer merge method changed so that sd limit is implemented before any…
shwilks May 12, 2023
9032f1b
Expose further optimization options as user controllable options
shwilks May 12, 2023
b69c06a
Add the option to set lighting using the r3js::light3js() function
shwilks May 12, 2023
1981b62
Add the option to set the viewer background color
shwilks May 12, 2023
41f55b8
Update documentation
shwilks May 12, 2023
5a968ae
Add argument in view.acmap to control set viewer background color
shwilks May 14, 2023
0e7bada
Match up arguments and documentation with generic method
shwilks May 14, 2023
a4ea0ca
Fix error where light was not being added to the viewer properly
shwilks May 16, 2023
8d53681
Add arguments to control procrustes arrow appearance in `plot.acmap()`
shwilks Jun 14, 2023
7c80ac2
Allow for shorthand description of shapes e.g. "C" for "CIRCLE" in ma…
shwilks Aug 29, 2023
ad8d18d
Add unexported functions to get map data in a long table format
shwilks Aug 29, 2023
97bc81f
Add unexported functions to get agExtra and srExtra information in a …
shwilks Aug 29, 2023
e76401a
Use R value color encoding for named colors
shwilks Aug 29, 2023
c53fb49
Update to version 1.2.5
shwilks Aug 29, 2023
5badadb
Add preliminary vignette describing styling a map
shwilks Aug 29, 2023
5b90034
Update animation function
shwilks Aug 29, 2023
eedfa70
Add customising map appearance vignette
shwilks Aug 29, 2023
8a2490b
Add tidyr
shwilks Aug 29, 2023
29fd09c
Add additional imports
shwilks Aug 29, 2023
9e201e5
Update Date
shwilks Aug 29, 2023
eee790d
Correct URL
shwilks Aug 29, 2023
840c305
Add CRAN submission notes
shwilks Aug 30, 2023
4e09543
Remove C++11 requirement
shwilks Aug 30, 2023
794df31
Set the default number of cores to use as 2 unless otherwise specified
shwilks Aug 30, 2023
09cea7a
Update to version 1.2.6
shwilks Aug 30, 2023
9b053cc
`on.exit()` calls added to code in `R/map_plot.R` and `inst/shinyapps…
shwilks Sep 1, 2023
9eef23d
Remove unused files
shwilks Sep 1, 2023
f0216ae
`snapshotMap()` function removed.
shwilks Sep 1, 2023
e47d869
Removed unused files
shwilks Sep 1, 2023
5f79bbb
Make sure user options are restored on exit
shwilks Sep 1, 2023
d97f47e
Remove test
shwilks Sep 1, 2023
cfa3173
Comment out benchmarking code
shwilks Sep 1, 2023
de6758c
Remove benchmarking code
shwilks Sep 1, 2023
00a13dd
Use testmap_large for tests instead of 2004 map
shwilks Sep 1, 2023
415e6ca
Update function documentation to make sure each function has a docume…
shwilks Sep 1, 2023
73d73b0
Ignore the vignettes/figures directory and the vignettes/intro-to-ant…
shwilks Sep 1, 2023
08b9c55
Update version and expand author and description
shwilks Sep 1, 2023
16f7d92
Update documentation
shwilks Sep 1, 2023
de47ece
Update news
shwilks Sep 1, 2023
6d2cd24
Add CRAN resubmission comments
shwilks Sep 1, 2023
6c1c5a9
Update submission info
shwilks Sep 1, 2023
28ec8d0
Update CRAN-SUBMISSION
shwilks Sep 1, 2023
6ff8b8c
Remove redundant author categories
shwilks Sep 1, 2023
427a0fc
specify graphics::par and add another on.exit call
shwilks Sep 1, 2023
5ffb2c1
Add documentation for the return value for the `view()` and `keepOpti…
shwilks Sep 4, 2023
fc41c6a
Remove unnecessary additional spaces in Description
shwilks Sep 4, 2023
68f1d63
Update cran-comments for new submission
shwilks Sep 4, 2023
2196763
Update cran submission file
shwilks Sep 4, 2023
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5 changes: 5 additions & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
^.*\.Rproj$
^.*\.code-workspace$
^\.Rproj\.user$
^doc$
^Meta$
Expand All @@ -13,3 +14,7 @@
^\.lintr$
^tests/testoutput$
^builds$
^CRAN-SUBMISSION$
^cran-comments\.md$
^vignettes/figures$
^vignettes/intro-to-antigenic-cartography\.Rmd$
29 changes: 10 additions & 19 deletions .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
Expand All @@ -18,7 +18,7 @@ jobs:
fail-fast: false
matrix:
config:
- {os: macOS-latest, r: 'release'}
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
Expand All @@ -29,30 +29,21 @@ jobs:
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: r-lib/actions/setup-pandoc@v1
- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v1
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: rcmdcheck
extra-packages: any::rcmdcheck
needs: check

- uses: r-lib/actions/check-r-package@v1

- name: Show testthat output
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash

- name: Upload check results
if: failure()
uses: actions/upload-artifact@main
- uses: r-lib/actions/check-r-package@v2
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
upload-snapshots: true
33 changes: 22 additions & 11 deletions .github/workflows/pkgdown.yaml
Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]
release:
types: [published]
workflow_dispatch:
Expand All @@ -12,24 +14,33 @@ name: pkgdown
jobs:
pkgdown:
runs-on: ubuntu-latest
# Only restrict concurrency for non-PR jobs
concurrency:
group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: r-lib/actions/setup-pandoc@v1
- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v1
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: pkgdown
extra-packages: any::pkgdown, local::.
needs: website

- name: Deploy package
run: |
git config --local user.name "$GITHUB_ACTOR"
git config --local user.email "[email protected]"
Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
- name: Build site
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
shell: Rscript {0}

- name: Deploy to GitHub pages 🚀
if: github.event_name != 'pull_request'
uses: JamesIves/[email protected]
with:
clean: false
branch: gh-pages
folder: docs
5 changes: 4 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,12 @@
*.sublime-workspace
*.o
*.o.tmp
src/.vscode/*
*.code-workspace
.vscode*
doc
inst/doc
Meta
tests/testoutput/*
docs
/doc/
/Meta/
3 changes: 3 additions & 0 deletions CRAN-SUBMISSION
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
Version: 1.2.7
Date: 2023-09-01 05:06:17 UTC
SHA: 427a0fcec70ce202358ed9f72e4a207d150cfb85
47 changes: 30 additions & 17 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,56 +1,69 @@
Package: Racmacs
Type: Package
Title: R Antigenic Cartography Macros
Version: 1.1.35
Date: 2022-02-23
Author: Sam Wilks
Maintainer: Sam Wilks <[email protected]>
Description: A toolkit for making antigenic maps from assay data such as HI assays.
Title: Antigenic Cartography Macros
Version: 1.2.7
Date: 2023-09-01
Authors@R:
c(person(given = "Sam",
family = "Wilks",
role = c("aut", "cre"),
email = "[email protected]"))
Description: A toolkit for making antigenic maps from immunological assay data,
in order to quantify and visualize antigenic differences between different
pathogen strains as described in
Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World
Health Organization influenza vaccine strain selection process. Additional
functions allow for the diagnostic evaluation of antigenic maps and an
interactive viewer is provided to explore antigenic relationships amongst
several strains and incorporate the visualization of associated genetic
information.
Depends: R (>= 4.0)
Imports:
Rcpp,
parallel,
jsonlite,
ks,
brotli,
shiny,
shinyFiles,
shinyjs,
htmlwidgets,
crayon,
ggplot2,
ggplot2 (>= 3.0.0),
htmltools,
rmarchingcubes,
shape,
ellipsis,
MASS,
lifecycle,
magrittr,
igraph,
brotli
dplyr,
vctrs,
rlang
LazyData: TRUE
Suggests:
testthat,
r3js,
knitr,
rmarkdown,
rstudioapi,
plotly,
geometry,
gdata,
stringr,
r3js,
tibble,
tidyr,
base64enc,
lifecycle,
MCMCpack
RoxygenNote: 7.1.2.9000
Roxygen: list(markdown = TRUE)
LinkingTo:
Rcpp,
RcppArmadillo,
RcppProgress,
RcppEnsmallen,
rapidjsonr
Remotes:
shwilks/r3js
Encoding: UTF-8
RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
URL: https://acorg.github.io/Racmacs, https://github.com/acorg/Racmacs
URL: https://acorg.github.io/Racmacs/, https://github.com/acorg/Racmacs/
BugReports: https://github.com/acorg/Racmacs/issues
License: AGPL-3
30 changes: 23 additions & 7 deletions NAMESPACE
Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
# Generated by roxygen2: do not edit by hand

S3method(drawDetails,acpoint)
S3method(ggplot,acmap)
S3method(plot,acmap)
S3method(postDrawDetails,acpoint)
S3method(preDrawDetails,acpoint)
S3method(print,Rac_html_merge_report)
S3method(print,acmap)
S3method(view,acmap)
Expand Down Expand Up @@ -85,6 +89,7 @@ export(agAnnotations)
export(agAspect)
export(agBaseCoords)
export(agBootstrapBlob)
export(agBootstrapBlobs)
export(agBootstrapCoords)
export(agClades)
export(agCohesion)
Expand All @@ -94,6 +99,7 @@ export(agDates)
export(agExtra)
export(agFill)
export(agGroups)
export(agHomologousSr)
export(agIDs)
export(agLabIDs)
export(agLeverage)
Expand All @@ -112,16 +118,17 @@ export(agShape)
export(agShown)
export(agSize)
export(agStress)
export(agStressBlobSize)
export(agStressPerTiter)
export(agStrings)
export(agTriangulationBlobSize)
export(agTriangulationBlob)
export(agTriangulationBlobs)
export(allMapDimensions)
export(allMapStresses)
export(applyMapTransform)
export(applyPlotspec)
export(as.json)
export(blob)
export(blobsize)
export(bootstrapBlobs)
export(bootstrapMap)
export(checkHemisphering)
Expand All @@ -133,7 +140,6 @@ export(edit_srNames)
export(export_viewer)
export(fixedColBases)
export(getOptimization)
export(grid.plot.acmap)
export(htmlAdjustedTiterTable)
export(htmlMergeReport)
export(htmlTiterTable)
Expand All @@ -143,6 +149,7 @@ export(keepSingleOptimization)
export(layerNames)
export(listOptimizations)
export(logtiterTable)
export(logtiterTableLayers)
export(make.acmap)
export(mapBootstrap_agCoords)
export(mapBootstrap_srCoords)
Expand Down Expand Up @@ -179,9 +186,11 @@ export(plotly_map_table_distance)
export(procrustesData)
export(procrustesMap)
export(ptBaseCoords)
export(ptBootstrapBlobs)
export(ptBootstrapCoords)
export(ptCoords)
export(ptDrawingOrder)
export(ptTriangulationBlobs)
export(randomizeCoords)
export(read.acmap)
export(read.titerTable)
Expand All @@ -201,12 +210,12 @@ export(save.acmap)
export(save.coords)
export(save.titerTable)
export(setLegend)
export(snapshotMap)
export(sortOptimizations)
export(srAnnotations)
export(srAspect)
export(srBaseCoords)
export(srBootstrapBlob)
export(srBootstrapBlobs)
export(srBootstrapCoords)
export(srClades)
export(srCohesion)
Expand All @@ -233,10 +242,10 @@ export(srShown)
export(srSize)
export(srSpecies)
export(srStress)
export(srStressBlobSize)
export(srStressPerTiter)
export(srStrings)
export(srTriangulationBlobSize)
export(srTriangulationBlob)
export(srTriangulationBlobs)
export(standardizeStrainNames)
export(stressBlobs)
export(stressTable)
Expand All @@ -251,5 +260,12 @@ export(triangulationBlobs)
export(update_ferret_seraNames)
export(view)
import(htmlwidgets)
importFrom(Rcpp,sourceCpp)
importFrom(Rcpp,`sourceCpp`)
importFrom(ggplot2,`.data`)
importFrom(ggplot2,`ggplot`)
importFrom(grid,`drawDetails`)
importFrom(grid,`postDrawDetails`)
importFrom(grid,`preDrawDetails`)
importFrom(magrittr,`%>%`)
importFrom(rlang,`.data`)
useDynLib(Racmacs)
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