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addDendrogramMarkers()
Add marker genes to reference dendrogram for tree mapping
addMapMyCells()
This function builds files needed for hierarchical mapping and stores them in the uns$hierarchical of AIT (Shiny) taxonomy.
buildTaxonomy()
This function builds the minimum files required for Shiny Precomputed clusters must be provided. In the anndata object these will be stored using the term "cluster". If hierarchy[-1] is anything other than cluster, then any existing "cluster" column will be overwritten by hierarchy[-1]. Values can be provided without colors and ids (e.g., "cluster") or with them (e.g., "cluster_label" + "cluster_color" + "cluster_id"). In this case cluster_colors is ignored and colors are taken directly from the metadata. Cluster_id's will be overwritten to match dendrogram order. (NOTE: Some functionality with metadata colors is still under development.)
buildTaxonomyMode()
Create a taxonomy mode for mapping to taxonomy subset (or child)
checkMetadata()
Checks whether metadata is in scrattch.taxonomy format
checkTaxonomy()
Checks whether an anndata object is in scrattch.taxonomy format and returns a log-file if not
computeOntologyTerms()
Updates a metadata data frame with ontology terms
cpm()
Convert a matrix of raw counts to a matrix of Counts per Million values
createShiny()
This function builds the minimum files required for Shiny
dend_to_json()
Convert R dendrogram to json
._transfer_factor_levels()
Convert one string back to a factor with matched, but different, values
file.path()
Construct Path to File across platforms
firsttolower()
Convert the first character of a string to lowercase
geneSymbolToEnsembl()
Convert gene symbols to Ensembl IDs
getNCBITaxon()
Determine the NCBITaxon ID for a species from the scientific name
get_cl_medians()
Compute cluster medians for each row in a matrix
json_to_dend()
Convert json to R dendrogram
loadTaxonomy()
Read in a reference data set in Allen taxonomy format
log2CPM_byRow()
Convert a matrix of raw counts to a matrix of log2(Counts per Million + 1) values
logCPM()
Convert a matrix of raw counts to a matrix of log2(Counts per Million + 1) values
mappingMode()
Function to set mapping mode
setLeadingString()
Sets the default leading_string for file.path()
setPathSeparator()
Sets the default path_separator for file.path()
subsampleCells()
Function to subsample cells
top_binary_genes()
Get top genes by beta (binary) score
tosentence()
Convert to sentence case
updateHighlyVariableGenes()
Function to add or update highly variable genes for the current mode
updateMarkerGenes()
Function to add or update marker genes for the current mode
updateTaxonomyMetadata()
Updates a metadata data frame to better align with the AIT schema