diff --git a/examples/test.R b/examples/test.R deleted file mode 100644 index 5a4b241..0000000 --- a/examples/test.R +++ /dev/null @@ -1,26 +0,0 @@ -## Load scrattch.mapping -library(scrattch.mapping) - -## Load in example count data -library(tasic2016data) - -## Compute log CPM -query.data = tasic_2016_counts -query.data = logCPM(query.data) - -## Specify which taxonomies to map against. -taxonomies = c("/allen/programs/celltypes/workgroups/rnaseqanalysis/shiny/10x_seq/human_BGplus_20211020") - -## Map data against all taxonomies -mapping.anno = list() -for(taxonomy in taxonomies){ - ## Load the shiny taxonomy into a standard object for mapping. - AIT.anndata = loadTaxonomy(refFolder = taxonomy) - ## Map! Returns a data.frame with mapping results. - mapping.anno[[taxonomy]] = taxonomy_mapping(AIT.anndata=AIT.anndata, - query.data=query.data, - label.cols="cluster_label", - corr.map=TRUE, - tree.map=TRUE, - seurat.map=TRUE) -} \ No newline at end of file