Optimizing a subset of antigens individually

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Racmacs
 Type: Package
 Title: R Antigenic Cartography Macros
-Version: 1.1.30
+Version: 1.1.35
 Date: 2022-02-23
 Author: Sam Wilks
 Maintainer: Sam Wilks <[email protected]>
@@ -24,7 +24,8 @@ Imports:
     ellipsis,
     MASS,
     lifecycle,
-    igraph
+    igraph,
+    brotli
 LazyData: TRUE
 Suggests: 
     testthat,

NAMESPACE

@@ -9,27 +9,30 @@ export("agAnnotations<-")
 export("agAspect<-")
 export("agBaseCoords<-")
 export("agClades<-")
+export("agContinent<-")
 export("agCoords<-")
 export("agDates<-")
 export("agExtra<-")
 export("agFill<-")
 export("agGroups<-")
 export("agIDs<-")
 export("agLabIDs<-")
+export("agLineage<-")
 export("agNames<-")
-export("agNamesAbbreviated<-")
-export("agNamesFull<-")
+export("agNucleotideSequences<-")
 export("agOpacity<-")
 export("agOutline<-")
 export("agOutlineWidth<-")
 export("agPassage<-")
 export("agReactivityAdjustments<-")
+export("agReassortant<-")
 export("agReference<-")
 export("agRotation<-")
 export("agSequences<-")
 export("agShape<-")
 export("agShown<-")
 export("agSize<-")
+export("agStrings<-")
 export("dilutionStepsize<-")
 export("fixedColBases<-")
 export("layerNames<-")
@@ -52,19 +55,22 @@ export("srFill<-")
 export("srGroups<-")
 export("srHomologousAgs<-")
 export("srIDs<-")
+export("srLineage<-")
 export("srNames<-")
-export("srNamesAbbreviated<-")
-export("srNamesFull<-")
+export("srNucleotideSequences<-")
 export("srOpacity<-")
 export("srOutline<-")
 export("srOutlineWidth<-")
 export("srPassage<-")
+export("srReassortant<-")
 export("srReference<-")
 export("srRotation<-")
 export("srSequences<-")
 export("srShape<-")
 export("srShown<-")
 export("srSize<-")
+export("srSpecies<-")
+export("srStrings<-")
 export("titerTable<-")
 export(RacMerge.options)
 export(RacOptimizer.options)
@@ -82,6 +88,7 @@ export(agBootstrapBlob)
 export(agBootstrapCoords)
 export(agClades)
 export(agCohesion)
+export(agContinent)
 export(agCoords)
 export(agDates)
 export(agExtra)
@@ -90,13 +97,14 @@ export(agGroups)
 export(agIDs)
 export(agLabIDs)
 export(agLeverage)
+export(agLineage)
 export(agNames)
-export(agNamesAbbreviated)
-export(agNamesFull)
+export(agNucleotideSequences)
 export(agOutline)
 export(agOutlineWidth)
 export(agPassage)
 export(agReactivityAdjustments)
+export(agReassortant)
 export(agReference)
 export(agRotation)
 export(agSequences)
@@ -106,6 +114,7 @@ export(agSize)
 export(agStress)
 export(agStressBlobSize)
 export(agStressPerTiter)
+export(agStrings)
 export(agTriangulationBlobSize)
 export(allMapDimensions)
 export(allMapStresses)
@@ -163,6 +172,7 @@ export(numSera)
 export(numSeraGroups)
 export(optimizeAgReactivity)
 export(optimizeMap)
+export(optimizeSubsetAgsIndividually)
 export(orderAntigens)
 export(orderSera)
 export(plot_map_table_distance)
@@ -209,21 +219,24 @@ export(srGroups)
 export(srHomologousAgs)
 export(srIDs)
 export(srLeverage)
+export(srLineage)
 export(srNames)
-export(srNamesAbbreviated)
-export(srNamesFull)
+export(srNucleotideSequences)
 export(srOutline)
 export(srOutlineWidth)
 export(srPassage)
+export(srReassortant)
 export(srReference)
 export(srRotation)
 export(srSequences)
 export(srShape)
 export(srShown)
 export(srSize)
+export(srSpecies)
 export(srStress)
 export(srStressBlobSize)
 export(srStressPerTiter)
+export(srStrings)
 export(srTriangulationBlobSize)
 export(standardizeStrainNames)
 export(stressBlobs)

NEWS.md

@@ -1,3 +1,4 @@
+
 # 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.
@@ -137,3 +138,27 @@
 # 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 1.1.32
+* 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 1.1.33
+* Add some basic support for viewing 1D maps
+* 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 1.1.34
+* Add support for getting and setting serum species with `srSpecies()`.
+* Redundant attributes `agNamesAbbreviated`, `agNamesFull`, `srNamesAbbreviated`, `srNamesFull` removed
+
+# Racmacs 1.1.35
+* Add antigen and sera attributes: `agLineage()`, `srLineage()`, `agReassortant()`, `srReassortant()`, `agStrings()`, `srStrings()`, `agContinent()`, `agNucleotideSequences()`, `srNucleotideSequences()` 

R/RcppExports.R

@@ -93,16 +93,24 @@ ac_ag_get_name <- function(ag) {
     .Call('_Racmacs_ac_ag_get_name', PACKAGE = 'Racmacs', ag)
 }
 
-ac_ag_get_name_full <- function(ag) {
-    .Call('_Racmacs_ac_ag_get_name_full', PACKAGE = 'Racmacs', ag)
+ac_ag_get_extra <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_extra', PACKAGE = 'Racmacs', ag)
 }
 
-ac_ag_get_name_abbreviated <- function(ag) {
-    .Call('_Racmacs_ac_ag_get_name_abbreviated', PACKAGE = 'Racmacs', ag)
+ac_ag_get_lineage <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_lineage', PACKAGE = 'Racmacs', ag)
 }
 
-ac_ag_get_extra <- function(ag) {
-    .Call('_Racmacs_ac_ag_get_extra', PACKAGE = 'Racmacs', ag)
+ac_ag_get_reassortant <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_reassortant', PACKAGE = 'Racmacs', ag)
+}
+
+ac_ag_get_strings <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_strings', PACKAGE = 'Racmacs', ag)
+}
+
+ac_ag_get_continent <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_continent', PACKAGE = 'Racmacs', ag)
 }
 
 ac_ag_get_match_id <- function(ag) {
@@ -149,16 +157,24 @@ ac_ag_set_name <- function(ag, value) {
     .Call('_Racmacs_ac_ag_set_name', PACKAGE = 'Racmacs', ag, value)
 }
 
-ac_ag_set_name_full <- function(ag, value) {
-    .Call('_Racmacs_ac_ag_set_name_full', PACKAGE = 'Racmacs', ag, value)
+ac_ag_set_extra <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_extra', PACKAGE = 'Racmacs', ag, value)
+}
+
+ac_ag_set_lineage <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_lineage', PACKAGE = 'Racmacs', ag, value)
 }
 
-ac_ag_set_name_abbreviated <- function(ag, value) {
-    .Call('_Racmacs_ac_ag_set_name_abbreviated', PACKAGE = 'Racmacs', ag, value)
+ac_ag_set_reassortant <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_reassortant', PACKAGE = 'Racmacs', ag, value)
 }
 
-ac_ag_set_extra <- function(ag, value) {
-    .Call('_Racmacs_ac_ag_set_extra', PACKAGE = 'Racmacs', ag, value)
+ac_ag_set_strings <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_strings', PACKAGE = 'Racmacs', ag, value)
+}
+
+ac_ag_set_continent <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_continent', PACKAGE = 'Racmacs', ag, value)
 }
 
 ac_ag_set_group <- function(ag, value) {
@@ -345,6 +361,10 @@ ac_sr_get_passage <- function(sr) {
     .Call('_Racmacs_ac_sr_get_passage', PACKAGE = 'Racmacs', sr)
 }
 
+ac_sr_get_species <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_species', PACKAGE = 'Racmacs', sr)
+}
+
 ac_sr_get_clade <- function(sr) {
     .Call('_Racmacs_ac_sr_get_clade', PACKAGE = 'Racmacs', sr)
 }
@@ -357,16 +377,24 @@ ac_sr_get_name <- function(sr) {
     .Call('_Racmacs_ac_sr_get_name', PACKAGE = 'Racmacs', sr)
 }
 
-ac_sr_get_name_full <- function(sr) {
-    .Call('_Racmacs_ac_sr_get_name_full', PACKAGE = 'Racmacs', sr)
+ac_sr_get_extra <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_extra', PACKAGE = 'Racmacs', sr)
 }
 
-ac_sr_get_name_abbreviated <- function(sr) {
-    .Call('_Racmacs_ac_sr_get_name_abbreviated', PACKAGE = 'Racmacs', sr)
+ac_sr_get_lineage <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_lineage', PACKAGE = 'Racmacs', sr)
 }
 
-ac_sr_get_extra <- function(sr) {
-    .Call('_Racmacs_ac_sr_get_extra', PACKAGE = 'Racmacs', sr)
+ac_sr_get_reassortant <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_reassortant', PACKAGE = 'Racmacs', sr)
+}
+
+ac_sr_get_strings <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_strings', PACKAGE = 'Racmacs', sr)
+}
+
+ac_sr_get_continent <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_continent', PACKAGE = 'Racmacs', sr)
 }
 
 ac_sr_get_match_id <- function(sr) {
@@ -401,6 +429,10 @@ ac_sr_set_passage <- function(sr, value) {
     .Call('_Racmacs_ac_sr_set_passage', PACKAGE = 'Racmacs', sr, value)
 }
 
+ac_sr_set_species <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_species', PACKAGE = 'Racmacs', sr, value)
+}
+
 ac_sr_set_clade <- function(sr, value) {
     .Call('_Racmacs_ac_sr_set_clade', PACKAGE = 'Racmacs', sr, value)
 }
@@ -413,16 +445,24 @@ ac_sr_set_name <- function(sr, value) {
     .Call('_Racmacs_ac_sr_set_name', PACKAGE = 'Racmacs', sr, value)
 }
 
-ac_sr_set_name_full <- function(sr, value) {
-    .Call('_Racmacs_ac_sr_set_name_full', PACKAGE = 'Racmacs', sr, value)
+ac_sr_set_extra <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_extra', PACKAGE = 'Racmacs', sr, value)
 }
 
-ac_sr_set_name_abbreviated <- function(sr, value) {
-    .Call('_Racmacs_ac_sr_set_name_abbreviated', PACKAGE = 'Racmacs', sr, value)
+ac_sr_set_lineage <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_lineage', PACKAGE = 'Racmacs', sr, value)
 }
 
-ac_sr_set_extra <- function(sr, value) {
-    .Call('_Racmacs_ac_sr_set_extra', PACKAGE = 'Racmacs', sr, value)
+ac_sr_set_reassortant <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_reassortant', PACKAGE = 'Racmacs', sr, value)
+}
+
+ac_sr_set_strings <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_strings', PACKAGE = 'Racmacs', sr, value)
+}
+
+ac_sr_set_continent <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_continent', PACKAGE = 'Racmacs', sr, value)
 }
 
 ac_sr_set_homologous_ags <- function(sr, value) {
@@ -469,8 +509,8 @@ ac_merge_tables <- function(maps, merge_options) {
     .Call('_Racmacs_ac_merge_tables', PACKAGE = 'Racmacs', maps, merge_options)
 }
 
-ac_merge_reoptimized <- function(maps, num_dims, num_optimizations, optimizer_options, merge_options) {
-    .Call('_Racmacs_ac_merge_reoptimized', PACKAGE = 'Racmacs', maps, num_dims, num_optimizations, optimizer_options, merge_options)
+ac_merge_reoptimized <- function(maps, num_dims, num_optimizations, min_col_basis, optimizer_options, merge_options) {
+    .Call('_Racmacs_ac_merge_reoptimized', PACKAGE = 'Racmacs', maps, num_dims, num_optimizations, min_col_basis, optimizer_options, merge_options)
 }
 
 ac_merge_frozen_overlay <- function(maps, merge_options) {

R/map_loadsave.R

@@ -30,7 +30,17 @@ read.acmap <- function(
 
   # Read the data from the file
   jsondata <- paste(readLines(filename, warn = FALSE), collapse = "\n")
-  map <- json_to_acmap(jsondata)
+  map <- tryCatch(
+    json_to_acmap(jsondata),
+    error = function(e) {
+      tryCatch(
+        read_brotli(filename),
+        error = function(e) {
+          stop("File '", filename, "' could not be parsed", call. = FALSE)
+        }
+      )
+    }
+  )
 
   # Apply arguments
   if (!is.null(optimization_number)) {
@@ -48,6 +58,13 @@ read.acmap <- function(
 
 }
 
+# Function to read brotli compressed maps
+read_brotli <- function(filepath) {
+  bin_file <- readBin(filepath, "raw", file.info(filepath)$size)
+  bin_uncompressed <- brotli::brotli_decompress(bin_file)
+  json_to_acmap(rawToChar(bin_uncompressed))
+}
+
 
 #' Save acmap data to a file
 #'