Merge pull request #33 from natverse/feature/malecns-lineage

Feature/malecns lineage

R/cosine.R

@@ -83,6 +83,11 @@ multi_cosine_matrix <- function(x, partners, nas, group='type') {
 #' @param drop_dataset_prefix Whether to remove dataset prefix such as
 #'   \code{hb:} or \code{fw:} from dendrograms. This is useful when reviewing
 #'   neurons in interactive mode.
+#' @param keep.all.meta Whether to keep all meta data information for the query
+#'   neurons to allow for more flexible labelling of the dendrogram (default
+#'   \code{TRUE} for convenience, so not really clear why you would want to set
+#'   to \code{FALSE}). See the \code{keep.all} argument of \code{\link{cf_meta}}
+#'   for details.
 #' @inheritParams cf_partners
 #' @inheritParams neuprintr::neuprint_cosine_plot
 #'
@@ -141,6 +146,10 @@ multi_cosine_matrix <- function(x, partners, nas, group='type') {
 #' ## on the build server, but similar queries could be run for multiple datasets
 #' cf_cosine_plot(cf_ids(flywire="/type:LAL.+", malecns="/type:LAL.+"))
 #'
+#' # we can use a range of dataset-specific columns to decorate labels
+#' cf_cosine_plot(cf_ids(flywire="/type:LAL0.+", hemibrain="/type:LAL0.+"),
+#'   labRow = "{top_nt}")
+#'
 #' cf_cosine_plot(cf_ids("/type:LAL.+", datasets='brain'))
 #' # same as since the default is brain
 #' cf_cosine_plot(cf_ids("/type:LAL.+"))
@@ -228,6 +237,7 @@ cf_cosine_plot <- function(ids=NULL, ..., threshold=5,
                            matrix=FALSE,
                            interactive=FALSE,
                            drop_dataset_prefix=FALSE,
+                           keep.all.meta=TRUE,
                            min_datasets=Inf,
                            nas=c('zero','drop'),
                            method=c("ward.D", "single", "complete", "average",
@@ -243,7 +253,7 @@ cf_cosine_plot <- function(ids=NULL, ..., threshold=5,
   cm <- multi_cosine_matrix(x, partners = partners, group=group, nas=nas)
 
   if(is.character(labRow) && length(labRow)==1 && any(grepl("\\{", labRow))) {
-    tm=cf_meta(colnames(cm))
+    tm=cf_meta(colnames(cm), keep.all = keep.all.meta)
     labRow <- glue::glue_data(labRow, .x = tm)
   } else if(is.character(labRow)) {
     # user has supplied labels but they are unlikely to be in the correct order

R/meta.R

@@ -49,7 +49,7 @@ cf_meta <- function(ids, bind.rows=TRUE, integer64=FALSE, keep.all=FALSE,
   if(is.data.frame(ids)) {
     stopifnot(bind.rows)
     ss=split(ids$id, ids$dataset)
-    res=cf_meta(ss, integer64 = integer64, MoreArgs = MoreArgs)
+    res=cf_meta(ss, integer64 = integer64, MoreArgs = MoreArgs, keep.all=keep.all)
     res=res[match(keys(ids), res$key),,drop=F]
     return(res)
   }
@@ -147,7 +147,10 @@ malecns_meta <- function(ids, ...) {
     rename(id=bodyid) %>%
     rename(class1=superclass, class2=class, subsubclass=subclass) %>%
     rename(class=class1, subclass=class2) %>%
-    rename(lineage=hemilineage)
+    mutate(lineage=case_when(
+      !is.na(itoleeHl) & nzchar(itoleeHl) ~ itoleeHl,
+      T ~ trumanHl
+    ))
   tres
 }