adding documentation for new GATAI functions #50

drostlab · Nov 20, 2024 · 6c7bd13 · 6c7bd13
1 parent 3563a77
commit 6c7bd13
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Showing 105 changed files with 1,025 additions and 255 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -7,6 +7,7 @@ export(EarlyConservationTest)
 export(EnrichmentTest)
 export(Expressed)
 export(FlatLineTest)
+export(GATAI)
 export(GroupDiffs)
 export(LateConservationTest)
 export(MatchMap)
@@ -27,13 +28,15 @@ export(PlotRE)
 export(PlotReplicateQuality)
 export(PlotSelectedAgeDistr)
 export(PlotSignature)
+export(PlotSignatureGATAIGeneRemoval)
 export(PlotSignatureTransformed)
 export(PlotVars)
 export(RE)
 export(REMatrix)
 export(ReductiveHourglassTest)
 export(ReverseHourglassTest)
 export(SelectGeneSet)
+export(SignatureGATAIGeneRemoval)
 export(TAI)
 export(TDI)
 export(TEI)
@@ -46,6 +49,7 @@ export(ecScore)
 export(geom.mean)
 export(harm.mean)
 export(is.ExpressionSet)
+export(is_installed_gatai)
 export(lcScore)
 export(omitMatrix)
 export(pMatrix)

diff --git a/R/GATAI.R b/R/GATAI.R
@@ -1,7 +1,5 @@
 #' @title Low level interface function with GATAI
-#' @description
-#' This function interfaces with the GATAI software which removes the genes that create the \code{\link{PlotSignature}} pattern.
-#' \code{GATAI} can be found at \url{https://github.com/drostlab/gatai}.
+#' @description This function interfaces with the GATAI software which removes the genes that create the \code{\link{PlotSignature}} pattern.
 #' @param ExpressionSet a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object.
 #' @param singlecell_data a logical value indicating whether or not the input \code{ExpressionSet} is a single cell dataset.
 #' @param gatai_results_path where shall GATAI results be stored. Default \code{gatai_results_path = tempdir()}.

diff --git a/R/PlotSignatureGATAIGeneRemoval.R b/R/PlotSignatureGATAIGeneRemoval.R
@@ -1,4 +1,4 @@
-#'  @title Plot evolutionary signatures across transcriptomes after GATAI gene removal
+#' @title Plot evolutionary signatures across transcriptomes after GATAI gene removal
 #' @description Main function to visualize transcriptome indices after GATAI gene removal  .
 #' @param ExpressionSet a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object.
 #' @param measure type of transcriptome index that shall be computed. E.g.

diff --git a/R/is_installed_gatai.R b/R/is_installed_gatai.R
@@ -1,4 +1,5 @@
 #' @title Test whether GATAI is installed on user machine
+#' @description Helper function to test if the user has set up GATAI correctly in their environment.
 #' @export
 is_installed_gatai <- function() {
   tryCatch({

diff --git a/config.log b/config.log
@@ -1,18 +1,2 @@
 0.29.2
 3
-using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
-using SDK: ‘’
-clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c test-omp.c -o test-omp.o
-test-omp.c:1:10: fatal error: 'omp.h' file not found
-#include <omp.h>
-         ^~~~~~~
-1 error generated.
-make: *** [test-omp.o] Error 1
-using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
-using SDK: ‘’
-clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c test-omp.c -o test-omp.o
-test-omp.c:1:10: fatal error: 'omp.h' file not found
-#include <omp.h>
-         ^~~~~~~
-1 error generated.
-make: *** [test-omp.o] Error 1
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/Advanced.html b/docs/articles/Advanced.html
diff --git a/docs/articles/Enrichment.html b/docs/articles/Enrichment.html
diff --git a/docs/articles/Expression.html b/docs/articles/Expression.html
diff --git a/docs/articles/Intermediate.html b/docs/articles/Intermediate.html
diff --git a/docs/articles/Introduction.html b/docs/articles/Introduction.html
diff --git a/docs/articles/Phylostratigraphy.html b/docs/articles/Phylostratigraphy.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -8,7 +8,7 @@ articles:
   Intermediate: Intermediate.html
   Introduction: Introduction.html
   Phylostratigraphy: Phylostratigraphy.html
-last_built: 2024-10-03T16:07Z
+last_built: 2024-11-20T09:19Z
 urls:
   reference: https://drostlab.github.io/myTAI/reference
   article: https://drostlab.github.io/myTAI/articles
diff --git a/docs/reference/CollapseReplicates.html b/docs/reference/CollapseReplicates.html
diff --git a/docs/reference/CombinatorialSignificance.html b/docs/reference/CombinatorialSignificance.html
diff --git a/docs/reference/DiffGenes.html b/docs/reference/DiffGenes.html
diff --git a/docs/reference/DivergenceExpressionSetExample.html b/docs/reference/DivergenceExpressionSetExample.html
diff --git a/docs/reference/EarlyConservationTest.html b/docs/reference/EarlyConservationTest.html
diff --git a/docs/reference/EnrichmentTest.html b/docs/reference/EnrichmentTest.html
diff --git a/docs/reference/Expressed.html b/docs/reference/Expressed.html