@@ -12,3 +12,4 @@ manuscript/

 .ignore

 README.Rmd

 data/ccdb_bcell.rda

+R/immcantation-utils.R

@@ -2,7 +2,7 @@ Type: Package

 Package: CellaRepertorium

 Title: Data structures, clustering and testing for single 

     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

-Version: 0.4.0

+Version: 0.8.0

 Authors@R: 

     c(person(given = "Andrew",

              family = "McDavid",

@@ -64,6 +64,7 @@ importFrom(rlang,":=")

 importFrom(rlang,sym)

 importFrom(rlang,syms)

 importFrom(stats,as.dist)

+importFrom(stats,as.formula)

 importFrom(stats,dist)

 importFrom(stats,hclust)

 importFrom(stats,na.fail)

@@ -1,3 +1,4 @@

+globalVariables('ngrp')

 #' Cluster contigs by germline properties

 #'

@@ -13,7 +14,8 @@

 #' ccdb_ex$cluster_tbl

 cluster_germline = function(ccdb, segment_keys = c('v_gene', 'j_gene', 'chain'), cluster_name = 'cluster_idx'){

     contig_tbl = ccdb$contig_tbl

-    seg_types = contig_tbl %>% group_by(!!!syms(segment_keys)) %>% summarize() %>% ungroup() %>% mutate(!!sym(cluster_name) := seq_len(nrow(.)))

+    seg_types = contig_tbl %>% group_by(!!!syms(segment_keys)) %>% summarize() %>% ungroup()

+    seg_types[[cluster_name]] = seq_len(nrow(seg_types))

     cl_con_tbl = left_join_warn(seg_types, contig_tbl, by = segment_keys)

     cluster_tbl = as_tibble(unique(cl_con_tbl[union(cluster_name, segment_keys)]))

     replace_cluster_tbl(ccdb, cluster_tbl, cl_con_tbl, cluster_pk = cluster_name)

@@ -151,7 +153,9 @@ tie_break_keys = character(), order = 1, representative = ccdb$cluster_pk[1], co

     arranging = purrr::map(tie_break_keys, ~ rlang::quo(desc(!!sym(.x))))

     # take first row of each cluster

-    cluster_tbl = sub_contig_tbl %>% group_by(!!!syms(ccdb$cluster_pk)) %>% dplyr::arrange(!!!arranging) %>% dplyr::do(dplyr::slice(., order))

+    cluster_tbl = sub_contig_tbl %>% group_by(!!!syms(ccdb$cluster_pk)) %>% dplyr::arrange(!!!arranging)

+    idx = cluster_tbl %>% transmute(ngrp = dplyr::n(), idx = seq_along(ngrp))

+    cluster_tbl = cluster_tbl[idx$idx==order,,drop = FALSE]

     cluster_tbl = cluster_tbl %>% dplyr::select(!!!syms(unique(c(ccdb$cluster_pk, contig_fields, representative))))

     # fill any missing clusters after the filtering

@@ -72,7 +72,9 @@ canonicalize_cell = function(ccdb, contig_filter_args = TRUE,  tie_break_keys =

     # setup quosures to arrange the data

     arranging = purrr::map(tie_break_keys, ~ rlang::quo(desc(!!sym(.x))))

     # take first row of each cell

-    ft2 = ft %>% group_by(!!!syms(ccdb$cell_pk)) %>% dplyr::arrange(!!!arranging) %>% dplyr::do(dplyr::slice(., order))

+    ft2 = ft %>% group_by(!!!syms(ccdb$cell_pk)) %>% dplyr::arrange(!!!arranging)

+    idx = ft2 %>% transmute(ngrp = dplyr::n(), idx = seq_along(ngrp))

+    ft2 = ft2[idx$idx==order,,drop = FALSE]

     cell_tbl = ccdb$cell_tbl

     # join with cell tbl (so same number of cells)

     ccdb$cell_tbl = right_join_warn(ft2[unique(c(contig_fields, ccdb$cell_pk))], cell_tbl, by = ccdb$cell_pk, overwrite = overwrite)