Search nearest neighbors — search

Search [shared] K-nearest neighbor graph to find the samples that are most similar to those matching a substring search.

search_neighbors(
  seurat,
  graph_name = NULL,
  var1_search = NULL,
  label_col = NULL,
  var2_group = NULL,
  group_col = NULL,
  max_neighbors = Inf,
  add_original_names = TRUE,
  verbose = TRUE
)

Arguments

seurat: Seurat object.
graph_name: Name of the graph to use. If none provided, will use the last graph available. If no graphs are available, new ones will be computed using Seurat::FindNeighbors.
var1_search: Substring search term to filter var1 by. If a vector is supplied instead, this will be interpreted as an "or" query.
label_col: meta.data column used to name the rows/columns of the graph. label_col will also be used in the search for var1_search substring.
var2_group: Substring search term to filter var2 by, according to group_col.
group_col: meta.data column used to filter var2 when var2_group is used.
max_neighbors: The max number of neighbors (var2) per term (var1).
add_original_names: Add original names into the results. This can be useful when var1 names are forced to be unique internally.
verbose: Whether to print messages.

Value

A data.table of pairwise similarities between query samples and their nearest neighbors.

Examples

data("pseudo_seurat")
top_neighbors <- search_neighbors(seurat = pseudo_seurat,
                                  var1_search = "purkinje",
                                  max_neighbors = 5)
#> No variable features detected. Computing
#> No PCA detected. Computing
#> Centering and scaling data matrix
#> PC_ 1 
#> Positive:  FTMT, ACTG1, ALAS2, HSPA1L, NME1-NME2, POTEI, OTOP2, RAPSN, BEST2, DPEP2 
#> 	   HMGB2, NAPRT1, KRT8, PPIB, DSCC1, POU4F3, CCDC102A, GAPDHS, CHST6, AGXT2 
#> 	   LYZL2, MTMR8, ACTG2, ACPL2, BANF1, PPAPDC2, HTR1A, IFI30, CYBRD1, LHX8 
#> Negative:  FAIM2, CAMK2A, SCN1A, CAMK2B, FRRS1L, UNC80, PHYHIP, RASGRF2, CCK, GRIA2 
#> 	   STXBP5L, ARPP21, SLC12A5, DIRAS2, RYR2, SLC4A10, KCNT1, GRM5, CAMKV, KIAA1211L 
#> 	   GABRA4, GABRA1, SV2B, CX3CL1, AK5, PNMA2, JPH4, DGKG, GPR158, KCNC2 
#> PC_ 2 
#> Positive:  CAMKK1, DGKQ, NT5DC3, CA7, ABCG4, HTR1A, C5orf28, OTOP2, HYKK, DPEP2 
#> 	   CHST6, POTEI, SLC8A3, SLC38A11, ADRA2A, MPPED1, MTMR8, HTR7, CACNA1B, PPAPDC2 
#> 	   C2orf69, GRIK1, IFI30, STK32B, RASL10B, SLC24A4, FAXDC2, ADCY3, ACSS2, ANKRD29 
#> Negative:  RAN, HSP90AA1, H2AFZ, HNRNPAB, CCT5, NPM1, GNG5, DBI, HMGB2, ITM2B 
#> 	   ATP6V1G1, SERPINH1, CIRBP, CD63, NDUFA6, MDK, JUN, MYL12B, SPARC, NPC2 
#> 	   GLUL, ID3, EEF1A1, VIM, CLIC1, COX6B1, LDHA, DDAH2, ENO1, CNN3 
#> PC_ 3 
#> Positive:  ADGRL2, AC011288.2, RP11-420N3.3, RP11-191L9.4, NRXN3, PLPPR1, RP11-123O10.4, ZNF385D, AC114765.1, NWD2 
#> 	   RBFOX3, MIR137HG, MIR325HG, SGOL1-AS1, POU6F2, ANKRD18A, LY86-AS1, LINC01197, DGCR5, DPY19L1P1 
#> 	   MIR4300HG, AQP4-AS1, HPSE2, LINC00632, NLGN4X, AC067956.1, PWRN1, LINC00599, CABP1, LINC01158 
#> Negative:  KRTCAP2, APOE, C20orf24, PDIA6, PGLS, GNG11, S100A13, HIST1H2BI, ISCA2, GSTM5 
#> 	   LAPTM4A, CST3, TMEM176B, KLF4, PDLIM2, CAP1, S100A16, APRT, CYR61, FAIM 
#> 	   IFITM3, CDKN1A, KLF2, CLIC1, ARPC1B, IER2, S100A1, CMTM5, FXYD1, TCN2 
#> PC_ 4 
#> Positive:  RESP18, CTXN2, ATP6V1G2, GNG13, DISP2, C15orf59, CCDC85A, GNG3, SYNGR3, RGS8 
#> 	   VWA5B2, C1QL3, HPCA, TUBB3, CALB1, SNCB, HTR3A, ARHGDIG, L1CAM, NAP1L5 
#> 	   PCDH20, HMP19, DBNDD2, NPAS4, FABP3, CALY, FAM43B, CKMT1B, LOC728392, LTK 
#> Negative:  PTPN18, SLCO1A2, LINC00639, INPP5D, IFI44, LYN, DISC1, NEAT1, NRGN, CMYA5 
#> 	   IFI44L, GALNT15, PARP14, AC012593.1, AQP4-AS1, MSR1, MT2A, ISG15, SHROOM4, CABP1 
#> 	   UACA, KCNQ1OT1, PART1, CNDP1, FAM153B, DGCR5, SOX2-OT, LINC00844, ADGRG1, LINC00599 
#> PC_ 5 
#> Positive:  MEST, IGFBP2, CNN3, FBXL7, NNAT, TUBB2B, GPC3, VIM, NKAIN4, ID1 
#> 	   BMP7, CSRP2, NDN, DDAH2, GPX8, IGFBPL1, MARCKSL1, GSTM3, FBLN1, PARD3 
#> 	   MFAP4, PTN, FABP7, COPS6, CTNNA2, ZBTB20, BEX1, CD81, ENO1, NPAS3 
#> Negative:  C1QB, FCGR2A, MS4A6A, TYROBP, C1QC, AIF1, C1QA, CSF1R, CD86, MRC1 
#> 	   MS4A7, CTSS, CCL24, FCER1G, CD53, CD14, FCGR1A, PLEK, C3AR1, LYZ 
#> 	   FCGR2B, CX3CR1, CCL3L3, CCL2, CCR1, CD68, C5AR1, PF4, HPGDS, LY86 
#> No graphs detected. Computing.
#> Computing nearest neighbor graph
#> Computing SNN
#> Using graph: RNA_snn
#> + Filtering results by `var1_search`: purkinje
#> + 3 entries matching `var1_search` identified.
#> + Adding original names to results
#> + Returning 19 pair-wise similarities.