Use readxl::read_excel() for reading excel files
instead of gdata::read.xls()
Racmacs 1.2.7
on.exit() calls added to code in
R/map_plot.R and
inst/shinyapps/RacmacsGUI/app.R where changes to graphical
parameters and user options are made.
snapshotMap() function removed.
Racmacs 1.2.6
Set the default number of cores to use as 2 unless otherwise
specified in either RacOptimizer.options, or by setting the global
option ‘RacOptimizer.num_cores’ with
e.g. options(RacOptimizer.num_cores = parallel::detectCores()).
Racmacs 1.2.5
Allow for shorthand description of shapes e.g. “C” for “CIRCLE” in
map .ace files.
Racmacs 1.2.4
Add arguments to control procrustes arrow appearance in
plot.acmap()
Racmacs 1.2.3
Fix error where light was not being added to the viewer
properly
Racmacs 1.2.2
Add argument in view.acmap to control set viewer background
color
Racmacs 1.2.1
Titer merge method changed so that sd limit is implemented before
any merging to < values
Expose further optimization options as user controllable
options
Add the option to set lighting using the r3js::light3js()
function
Add the option to set the viewer background color
Racmacs 1.2.0
Add new options and default methods to use when merging titers as
described for RacMerge.options()
Return a more useful error if bootstrapBlobs() is run
on a map where bootstrapMap() has not yet been
performed.
Add grid.margin.lwd option to control grid margin
linewidth in ggplot(map)
Improve user interruption of map optimization runs
Racmacs 1.1.40
Add some options to view.acmap to set the starting viewer
translation, rotation and zoom
Add grid.lwd option to control grid linewidth in
ggplot(map)
Add antigen and sera names to vector when retrieving antigen and
sera attributes like agFill()
Racmacs 1.1.39
Correct error when plotting cases where blobs were calculated for
only 1 antigen / serum
Only show plot outlier arrowheads if point is marked as shown
Numeric table distances account for dilution stepsize setting of
map
Racmacs 1.1.38
Add option to specify a subset of antigens and sera for which to
calculate blobs in the bootstrapBlobs() function
Add method for plotting a map using ggplot
i.e. ggplot(map).
When coloring by sequence a more distinct color palette is used
Racmacs 1.1.37
Fix error where serum column base label would remain after turning
titer labels off
Set default margins of 0.5 inches when plotting a map
Add support for insertions in amino acids sequences
Racmacs 1.1.36
Fix error in reoptimized-merge
logtiterTableLayers() function exported
Fix error when blobs are smaller than grid-spacing used to calculate
them
Add the blobsize() function for calculating the
area/volume of uncertainty blobs
Removed function triangulationBlobSize() - now use
e.g. sapply(agTriangulationBlobs(map), blobsize)
3D blob meshes are now separated into a list of contiguous meshes so
that number of blobs can be retrieved from the length,
i.e. sapply(agTriangulationBlobs(map), length)
Racmacs 1.1.35
Add antigen and sera attributes: agLineage(),
srLineage(), agReassortant(),
srReassortant(), agStrings(),
srStrings(), agContinent(),
agNucleotideSequences(),
srNucleotideSequences()
Racmacs 1.1.34
Add support for getting and setting serum species with
srSpecies().
Fix an issue viewing sequence data where sequence data is not
present for all antigens / sera
Fix an error reoptimize merging maps with no optimizations
Add verbosity argument to mergeMaps()
Verbosity argument also suppresses optimization progress
messages
Issue a warning if duplicate antigen or serum names are found when
creating a map
Racmacs 1.1.32
Disconnected maps now return an error rather than a warning
agStressPerTiter() and srStressPerTiter()
now return a matrix with columns corresponding to stress per titer when
nd values are excluded and when they are included
Corrected error when coloring maps by stress or showing error lines
with disconnected points
If a titer table has column or row names but not sera or antigen
names provided, names will be taken from the row and column names when
creating a map.
Add support for reading maps with brotli compression
agSequences() and srSequences() now works
when the stored sequences have different lengths or are missing for some
points
Correct error where maps with duplicate antigen or serum names would
not optimize
Racmacs 1.1.31
Added checks for disconnected groups of points and functions
mapCohesion(), agCohesion(),
srCohesion() to diagnose poorly connected groups of
points
Add support for point transparency set either through
agOpacity() and srOpacity() or appropriate hex
code to the point fill or outline attribute
e.g. "#FF000099".
Racmacs 1.1.30
Added support for setting indices of homologous antigens for sera
with srHomologousAgs()
Racmacs 1.1.29
mergeMaps() now accepts maps as either separate
arguments mergeMaps(map1, map2) or as a list
mergeMaps(list(map1, map2))
Additional checks for antigen and serum attribute inputs
Error corrected where merging maps with multiple titer layers caused
session to crash
Racmacs 1.1.28
agStress() and srStress() fixed to work
with NA coordinates
Correct error when calculating agStressPerTiter() and
srStressPerTiter() with missing titers.
Antigen/Sera sequence and date information now write to json fields
in line with acmacs-web.
Add attribute getters and setters agAnnotations(),
srAnnotations(), agLabIDs()
Racmacs 1.1.27
logtiterTable() nows returns a table with named columns
and rows
Fix issue showing individual bootstrap points in 3D
Add option show_group_legend to view() to
show interactive legend based on agGroups() and
srGroups() point groupings
Add ability in viewer to filter and color antigens and sera by
group
Racmacs 1.1.26
Add option to select the algorithm MASS::kde2d or ks::kde for
calculating 2D density blobs.
Add functions to help plot and inspect bootstrap blobs,
agBootstrapBlob(), srBootstrapBlob(),
agBootstrapCoords(), srBootstrapCoords(),
blob()
Racmacs 1.1.25
Throw an error instead of crashing when trying to do procrustes on
maps with duplicate antigen/sera names/ids
Add option to extend density blobs for e.g. bootstrapBlobs to extend
beyond the range of the actual coordinates.
Racmacs 1.1.24
Regions outside of plot border will now be masked when running
plot() on a map
Racmacs 1.1.23
Fix subsetMap() to also subset ag reactivity
adjustments!
Racmacs 1.1.22
agReactivityAdjustments now becomes a property of the
base acmap object rather than individual optimization runs
Racmacs 1.1.21
Full precision used in rapidjson when parsing doubles to load and
save maps
Added numSeraGroups() function
Added “extra” field for antigens and sera, and corresponding
agExtra() and srExtra() functions
Antigen and serum groups will now be maintained and merged when
running mergeMaps()
Where maps have shared dilutionStepsize() settings,
this will be applied to the merged map. Alternatively a warning will be
issued and a default setting of 1 applied where they have different
dilutionStepsize() settings.
Add attribute getter numLayers() for returning the
number of titer table layers in a map.
titerTable()<- will now throw an error if the titer
table applied does not have the same dimensions as the map in terms of
number of antigens and sera
When maps are merged the mapName will be used to name
the titer table layers, layer names can also be get and set directly
using the new layerNames() function
Racmacs 1.1.20
Slight re-implementation of dimensional annealing to not report
progress bar multiple times.
Added ability to include and exclude antigens and sera when
optimizing in the javascript viewer by alt clicking the name in the
browser or the titer in the interactive titer table.
Added ability in the javascript viewer to change the antigen
reactivity adjustment by selecting the antigen and editing the value as
it appears in the diagnostics tab.
Use quicker algorithm for calculating 2d density blobs
Dimension testing now calculates proportion of titers to exclude as
test set as proportion of measured titers, not proportion of detectable
titers.
Fixes an error when only one blob would be displayed in the viewer
in cases where more than one blob was associated with a point
Speed improvements to the calculation of contour blobs from point
densities in 2-dimensions
Added the option to set a description field for the map with the
mapDescription() function
Racmacs 1.1.19
Add option to procrustesData() to included only
specific antigens or sera, as can already be done for
procrustesMap()
Add methods to calculate point leverage, the effect of removing
different strains and sera from the map, agLeverage(),
srLeverage(), titerLeverage()
Change the view.acmap() method to allow for an option
num_optimizations to specify how many optimizations to send
to the viewer.
Add an option for and basic check by default for convergence of
solutions when running map optimizations.
Racmacs 1.1.18
Add option to edit titers in the titer table view and fix previous
error that had been introduced stopping the table view
Fix the map viewer stress calculations to account for the new
“dilution stepsize” setting
Add option to get and set antigen reactivity in the viewer
Fix an error that was causing NAs to appear in transformed
coordinates in linux builds
Racmacs 1.1.17
Added htmlMergeReport() showing how titers were merged
as a formatted html table.
Added htmlTiterTable() for visualizing an html
formatted titer table
Added functions for getting titers after applying antigen reactivity
adjustments set with agReactivityAdjustments()<-, namely
adjustedTiterTable(), adjustedLogTiterTable(),
htmlAdjustedTiterTable()
Details are no longer saved in map json if they are map
defaults
Added an option to round titers to the nearest unit when outputting
(for e.g. listmds compatibility)
Adds the ability to apply and set scaling on an optimization
Add option to optimize from scratch when performing
optimizeAgReactivity
Fix an error when performing procrustes with some coordinates set to
NA
Fix an error where transforming na coordinates in the viewer would
give a numeric value
Add an option to use arrowheads rather than arrows to show outlier
points when plotting
Racmacs 1.1.16
Fix error when minimum column basis is set to higher than any
measurable titer
Points not included in a procrustes will now be faded out when
plotted with plot(), similar to the behaviour already
implemented in the view() function.
Added the ability to set merge options when merging maps,
controlling for example how much standard deviation there has to be
between merged titers before the merged titer gets excluded as
unreliable.
Added mergeReport() and htmlMergeReport()
to output formatted tables showing how different titers have been merged
in a merged map.
Functions like logtiterTable() and
mergeMaps() now take account of the dilutionStepsize map
setting
Implement a new titer type ‘.’, like ’*’ but to represent titers
that are missing as a result of antigen sera combinations not being
present in merged tables
Fix error calculating bootstrap blobs and showing from a
bootstrapped map where “resample” method was used
Racmacs 1.1.15
Add option to set dilutionStepsize() for cases where
dilution series did not follow 2-fold dilution steps
Racmacs 1.1.14
Add option to save map in uncompressed format
Add option to output json in pretty format
Set default grid margin color to slightly darker than the grid
color
Correct error showing column bases in the viewer
Racmacs 1.1.13
Add option in plot.acmap() to draw stress lines
Add xlim and ylim options to view.acmap() to control
how maps are displayed
Add check to procrustes that there are sufficient matching
points
Racmacs 1.1.12
Fix error in Racmacs when calculating antigen and sera mean stress
per titer
Fix error in viewer code when accounting for antigen reactivity
adjustments in stress calculations
Racmacs 1.1.11
Added a NEWS.md file to track changes to the
package.
Added test and correction for error where coordinates of
under-constrained points were set to NaN for the first optimization run
only, not all.
Added integrated support for setting antigen reactivity
adjustments
Fixed error displaying bootstrap and triangulation blobs for maps
that had been rotated
Bootstrap blobs will now show when doing a standard map plot
Added ability to control grid size when calculating bootstrap blobs,
controlling how finely they are calculated
Added function optimizeAgReactivityAdjustments() for
optimizing antigen reactivity adjustments
Added function agReactivityAdjustments() for getting
and setting reactivity adjustments
Updated threejs library
Fixed bug where points were displayed in incorrect positions in the
viewer when the webgl maximum point size had been reached
Added button to toggle point labels on and off
Fixed error where ace files with no plotspec field would not read
in
Allow logical specification of antigens and sera for functions like
removeAntigens()
Check you do not try and remove all antigens or sera
Added option to show map stress in plot
Added ability to relax map points directly from the javascript
viewer
Added the function mapGadget() for opening up a map
object in the GUI
Fix error causing 3d arrows to not display
Update the way point stress and residual is calculated for the
stress and residual error table
Added option to plot.acmap to indicate points outside of plot limits
with an arrow