Nothing
splitTiterLayers()
now exported.readxl::read_excel()
for reading excel files instead of gdata::read.xls()
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.options(RacOptimizer.num_cores = parallel::detectCores())
.plot.acmap()
RacMerge.options()
bootstrapBlobs()
is run on a map where bootstrapMap()
has not yet been performed.grid.margin.lwd
option to control grid margin linewidth in ggplot(map)
grid.lwd
option to control grid linewidth in ggplot(map)
agFill()
bootstrapBlobs()
functionggplot(map)
.logtiterTableLayers()
function exportedblobsize()
function for calculating the area/volume of uncertainty blobstriangulationBlobSize()
- now use e.g. sapply(agTriangulationBlobs(map), blobsize)
sapply(agTriangulationBlobs(map), length)
agLineage()
, srLineage()
, agReassortant()
, srReassortant()
, agStrings()
, srStrings()
, agContinent()
, agNucleotideSequences()
, srNucleotideSequences()
srSpecies()
.agNamesAbbreviated
, agNamesFull
, srNamesAbbreviated
, srNamesFull
removedmergeMaps()
agStressPerTiter()
and srStressPerTiter()
now return a matrix with columns corresponding to stress per titer when nd values are excluded and when they are includedagSequences()
and srSequences()
now works when the stored sequences have different lengths or are missing for some pointsmapCohesion()
, agCohesion()
, srCohesion()
to diagnose poorly connected groups of pointsagOpacity()
and srOpacity()
or appropriate hex code to the point fill or outline attribute e.g. "#FF000099"
.srHomologousAgs()
mergeMaps()
now accepts maps as either separate arguments mergeMaps(map1, map2)
or as a list mergeMaps(list(map1, map2))
agStress()
and srStress()
fixed to work with NA coordinatesagStressPerTiter()
and srStressPerTiter()
with missing titers.agAnnotations()
, srAnnotations()
, agLabIDs()
logtiterTable()
nows returns a table with named columns and rowsshow_group_legend
to view()
to show interactive legend based on agGroups()
and srGroups()
point groupingsagBootstrapBlob()
, srBootstrapBlob()
, agBootstrapCoords()
, srBootstrapCoords()
, blob()
plot()
on a mapsubsetMap()
to also subset ag reactivity adjustments!agReactivityAdjustments
now becomes a property of the base acmap object rather than individual optimization runsnumSeraGroups()
functionagExtra()
and srExtra()
functionsmergeMaps()
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.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 seramapName
will be used to name the titer table layers, layer names can also be get and set directly using the new layerNames()
functiondiagnostics
tab.mapDescription()
functionprocrustesData()
to included only specific antigens or sera, as can already be done for procrustesMap()
agLeverage()
, srLeverage()
, titerLeverage()
view.acmap()
method to allow for an option num_optimizations
to specify how many optimizations to send to the viewer.htmlMergeReport()
showing how titers were merged as a formatted html table.htmlTiterTable()
for visualizing an html formatted titer tableagReactivityAdjustments()<-
, namely adjustedTiterTable()
, adjustedLogTiterTable()
, htmlAdjustedTiterTable()
plot()
, similar to the behaviour
already implemented in the view()
function.mergeReport()
and htmlMergeReport()
to output formatted tables showing how different titers have
been merged in a merged map.logtiterTable()
and mergeMaps()
now take account of the dilutionStepsize map settingdilutionStepsize()
for cases where dilution series did not follow 2-fold dilution stepsplot.acmap()
to draw stress linesview.acmap()
to control how maps are displayedNEWS.md
file to track changes to the package.optimizeAgReactivityAdjustments()
for optimizing antigen reactivity adjustmentsagReactivityAdjustments()
for getting and setting reactivity adjustmentsremoveAntigens()
mapGadget()
for opening up a map object in the GUIAny scripts or data that you put into this service are public.
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