Detect features that are spatially correlated. Functions for
starting from either a gobject (detectSpatialCorFeats()) or individual
pieces of data (detectSpatialCorFeatsMatrix()) are provided.
detectSpatialCorFeats(
gobject,
spat_unit = NULL,
feat_type = NULL,
spat_loc_name = "raw",
method = c("grid", "network"),
expression_values = c("normalized", "scaled", "custom"),
subset_feats = NULL,
spatial_network_name = "Delaunay_network",
network_smoothing = NULL,
spatial_grid_name = "spatial_grid",
min_cells_per_grid = 4,
cor_method = c("pearson", "kendall", "spearman")
)
detectSpatialCorFeatsMatrix(
expression_matrix,
method = c("grid", "network"),
spatial_network,
spatial_grid,
spatial_locs,
subset_feats = NULL,
network_smoothing = NULL,
min_cells_per_grid = 4,
cor_method = c("pearson", "kendall", "spearman")
)giotto object
spatial unit
feature type
name for spatial locations
method to use for spatial averaging
gene expression values to use
subset of features to use
name of spatial network to use
smoothing factor between 0 and 1 (has automatic default, see details)
name of spatial grid to use
minimum number of cells to consider a grid
correlation method
provided expression matrix
provided spatial network
provided spatial grid
provided spatial locations
returns a spatial correlation object: spatCorObject
For method = network, it expects a fully connected spatial network.
You can make sure to create a
fully connected network by setting minimal_k > 0 in the
createSpatialNetwork function.
grid-averaging: average gene expression values within a predefined spatial grid
network-averaging: smoothens the gene expression matrix by
averaging the expression within one cell by using the neighbours within
the predefined spatial network. \(b\) is a smoothening factor passed by
network_smoothing param that defaults to \(1 - 1/k\), where \(k\)
is the median number of k-neighbors in the selected spatial network.
Setting \(b = 0\) means no smoothing and \(b = 1\) means no
contribution from its own expression.
The spatCorObject can be further explored with showSpatialCorFeats()
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#> active environment : '/usr/bin/python3'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/bin/python3"
# Perform with data in a gobject
detectSpatialCorFeats(g, method = "network")
#> $cor_DT
#> feat_ID variable spat_cor expr_cor cordiff spatrank
#> <char> <fctr> <num> <num> <num> <int>
#> 1: 1110017D15Rik 1110017D15Rik 1.0000000 1.0000000 0.00000000 1
#> 2: 1110017D15Rik Dnali1 0.5152451 0.3690438 0.14620131 2
#> 3: 1110017D15Rik Spag8 0.5044653 0.3180572 0.18640810 3
#> 4: 1110017D15Rik 1700001C02Rik 0.4957575 0.4021766 0.09358091 4
#> 5: 1110017D15Rik Ccdc153 0.4947645 0.4050736 0.08969090 5
#> ---
#> 401952: Zmat4 Cabp7 -0.3106553 -0.2099353 -0.10072002 630
#> 401953: Zmat4 Sst -0.3310337 -0.1903481 -0.14068568 631
#> 401954: Zmat4 Hopx -0.3886083 -0.2587739 -0.12983435 632
#> 401955: Zmat4 Ttr -0.4280274 -0.3482754 -0.07975206 633
#> 401956: Zmat4 Gfap -0.4757224 -0.3562773 -0.11944508 634
#> exprrank rankdiff
#> <int> <int>
#> 1: 1 0
#> 2: 6 -4
#> 3: 10 -7
#> 4: 3 1
#> 5: 2 3
#> ---
#> 401952: 630 0
#> 401953: 627 4
#> 401954: 632 0
#> 401955: 633 0
#> 401956: 634 0
#>
#> $feat_order
#> [1] "Gna12" "Ccnd2" "Btbd17" "Sox9"
#> [5] "Sez6" "Serpinf1" "S100a6" "Col1a1"
#> [9] "Vwf" "Esam" "Npas1" "Tiam1"
#> [13] "Bcam" "Hmgn2" "Rab3b" "Inmt"
#> [17] "Ddr1" "Homer3" "Cp" "Calb2"
#> [21] "Man1a" "Efnb3" "Hlf" "Gstm7"
#> [25] "Cavin1" "Sst" "Hapln2" "Hspb1"
#> [29] "Ndrg1" "Nid1" "Kit" "Pvalb"
#> [33] "Tmbim1" "Crip1" "Tek" "Elovl1"
#> [37] "Cyba" "Itih3" "Cnp" "Hap1"
#> [41] "Clic1" "Stx1a" "Arpp19" "Dio2"
#> [45] "Id3" "Crlf1" "Ttc9b" "Carhsp1"
#> [49] "Cabp7" "Fam163b" "Rarres2" "Syn2"
#> [53] "Ick" "Prox1" "Adssl1" "Vipr2"
#> [57] "Gltp" "Amotl1" "Bcas1" "Aldh1a2"
#> [61] "Tppp3" "Sirt2" "Lpl" "Cers2"
#> [65] "Qdpr" "Stk32c" "Lbp" "Hsd11b1"
#> [69] "Vtn" "Stac2" "Plxdc1" "Igfbp4"
#> [73] "Dbndd2" "Pltp" "Slc12a4" "Cadps2"
#> [77] "Erbb3" "Pmp22" "Kcnab3" "Myh11"
#> [81] "Plod1" "Etnppl" "Arhgef25" "Rcn3"
#> [85] "Vip" "Utrn" "Grm1" "Reep3"
#> [89] "Fabp7" "Dcn" "Slc17a8" "Dusp6"
#> [93] "Kitl" "Ccn2" "Timp3" "Ascl1"
#> [97] "Unc5b" "Vsir" "Gamt" "Ptprb"
#> [101] "Csrp2" "Adarb1" "Rnf130" "Nefh"
#> [105] "Aebp1" "Sept4" "Gria1" "Sypl"
#> [109] "Arsg" "Cacng4" "Rab37" "Itgb4"
#> [113] "Aspa" "Cygb" "Rflnb" "Doc2b"
#> [117] "Gfap" "Npas3" "Serpina3n" "Clmn"
#> [121] "Prkch" "Fbln5" "Akr1c18" "Gng4"
#> [125] "Sema4d" "Cxcl14" "Hexb" "Iqgap2"
#> [129] "Crhbp" "Rab3c" "Thbs4" "Serinc5"
#> [133] "Erbin" "Prkcd" "Pdlim2" "Ednrb"
#> [137] "Cpne6" "Sema5a" "Matn2" "Nptxr"
#> [141] "Enpp2" "Efcab6" "Ppp1r1a" "Litaf"
#> [145] "Il1rap" "Apod" "Cpox" "Grik1"
#> [149] "Clic6" "Nr4a1" "Igfbp6" "Sncg"
#> [153] "Gzma" "Grm2" "Prph" "Rsph1"
#> [157] "Sox8" "Fam234a" "Lims2" "Aqp4"
#> [161] "Slc12a2" "Cd74" "Pdgfrb" "Csf1r"
#> [165] "Cbln2" "Frmd8" "Gldc" "Tcf7l2"
#> [169] "Bhlhe22" "Kcnip2" "Alas2" "Gdf11"
#> [173] "Baiap2" "Ifitm3" "Phkg1" "Nptx1"
#> [177] "Pde8a" "Itih5" "Homer2" "Fam20c"
#> [181] "Cplx2" "Myo5b" "Snca" "Col3a1"
#> [185] "Ecrg4" "Map4k4" "2010300C02Rik" "Ogfrl1"
#> [189] "Fn1" "Efhd1" "Ngef" "Bok"
#> [193] "Tmem163" "Lct" "Cfh" "Ptpn4"
#> [197] "Tnni1" "Csrp1" "Nfasc" "Syt2"
#> [201] "Atp2b4" "Rgs16" "Ncf2" "Cnih3"
#> [205] "Tmem63a" "Cfap126" "Meig1" "Ccdc3"
#> [209] "Rgs5" "Enkur" "Myoc" "Vim"
#> [213] "Prkcq" "Gad2" "Lcn2" "Nr4a2"
#> [217] "Ermn" "Fibcd1" "Gsn" "Grb14"
#> [221] "Notch1" "Ube2l6" "Gatm" "Cd82"
#> [225] "Mdk" "Lamp5" "Itpka" "Chgb"
#> [229] "Mal" "Pdyn" "Nkx2-2" "Edn3"
#> [233] "Car2" "Col9a3" "Chrna4" "Gss"
#> [237] "Slc7a11" "Tm4sf1" "Kcnab1" "Shox2"
#> [241] "Serpini1" "Tspan2" "S100a11" "Vcam1"
#> [245] "Lef1" "Npy2r" "F3" "Calb1"
#> [249] "Epha7" "Slc44a1" "1110017D15Rik" "Tpm2"
#> [253] "Slc6a9" "Laptm5" "Sema3c" "Hpca"
#> [257] "Padi2" "Slc4a2" "Gabrd" "Rgs12"
#> [261] "Slc30a3" "Emilin1" "1700001C02Rik" "Gabra4"
#> [265] "Pdgfra" "Epha5" "Tesc" "Pitpnm2"
#> [269] "Mmp17" "Cit" "Foxp2" "Arpc1b"
#> [273] "Col1a2" "Eln" "Pcolce" "Tsc22d4"
#> [277] "Cald1" "Ccdc136" "Npy" "Slc13a4"
#> [281] "Gkn3" "Slc6a13" "Mgp" "Lmo3"
#> [285] "Slco1c1" "Cpne9" "Itpr2" "Slc6a11"
#> [289] "Vamp1" "Cd9" "Pglyrp1" "Slc17a6"
#> [293] "Sipa1l3" "Sh3gl3" "Plekhb1" "Nupr1"
#> [297] "Dkk3" "Cox6a2" "Dkkl1" "Fgfr2"
#> [301] "Crym" "Slc38a5" "Flna" "Bgn"
#> [305] "Col4a1" "Plat" "Nr3c2" "Cbln1"
#> [309] "Gab1" "Pllp" "Necab2" "Dbndd1"
#> [313] "Agt" "Cryab" "Tagln" "Mcam"
#> [317] "Olfm2" "Icam5" "Anxa2" "Rora"
#> [321] "Calml4" "Htr3a" "Paqr5" "Rasgrf1"
#> [325] "Zic1" "Mobp" "Hhatl" "Trf"
#> [329] "Cpne4" "Cdhr4" "Cd59a" "Gng11"
#> [333] "Chrm1" "Prr5l" "Ugt8a" "Rims3"
#> [337] "Sgpp2" "Camkv" "Sox10" "Micall1"
#> [341] "Tie1" "Fa2h" "Ucp2" "Vav3"
#> [345] "Ccp110" "Gria2" "Rasl10a" "Foxj1"
#> [349] "Trim59" "Dynlrb2" "Gjc1" "Neurod1"
#> [353] "Ttyh2" "Cpne7" "Nrip3" "Tbr1"
#> [357] "Lcat" "Tmem98" "Myo1d" "Prdm8"
#> [361] "Tgfbi" "Kcnc2" "Thrsp" "Isg15"
#> [365] "Acta2" "H2-Q4" "Dock4" "Myrf"
#> [369] "Lmo1" "Igfbp7" "P2ry12" "Pcdh8"
#> [373] "Lgi4" "Fxyd1" "Fxyd7" "Mag"
#> [377] "Zcchc12" "Anln" "Wnt4" "C1ql2"
#> [381] "Unc93b1" "Tspan15" "Ppp1r14a" "Clic4"
#> [385] "Galnt6" "Ccn3" "Rims2" "Zmat4"
#> [389] "Cldn11" "Ccdc33" "Slc32a1" "Tgm2"
#> [393] "Vstm2l" "Neurod6" "Crygn" "Enpp6"
#> [397] "Neurod2" "Satb2" "Pcp4l1" "Txnip"
#> [401] "Egr1" "Otud7b" "Car14" "Rgs4"
#> [405] "Dock10" "Lpar1" "Trps1" "Ptpn3"
#> [409] "Lefty1" "Zfhx3" "St6galnac5" "Ak5"
#> [413] "Hrh3" "Nexn" "Adgrl4" "Rlbp1"
#> [417] "Igfbp2" "Wfs1" "Cplx3" "Orai2"
#> [421] "Olig2" "Gpr37" "Plcb4" "Nxph4"
#> [425] "Ndufa4l2" "Cacng5" "Plekhg1" "Cmtm5"
#> [429] "Gpr161" "Rfx3" "Igsf21" "Ramp3"
#> [433] "Arhgap12" "Nkx6-2" "Ninj2" "Cldn5"
#> [437] "Htr2c" "Hspb8" "Fmod" "Prelp"
#> [441] "Mpped1" "Rapgef5" "Vwa1" "Stab1"
#> [445] "Arl15" "Reln" "Mustn1" "Pbxip1"
#> [449] "Dnali1" "Id1" "Lrrtm3" "Tmem212"
#> [453] "Epop" "Gjc2" "1190005I06Rik" "Ctla2a"
#> [457] "Cnr1" "Gpr4" "Sowaha" "Tent5c"
#> [461] "Serpinb1a" "S1pr5" "Penk" "Cdc42ep2"
#> [465] "Slitrk6" "Hpcal4" "Olig1" "Rprml"
#> [469] "Stxbp6" "Hs3st2" "Rbp1" "Ppm1e"
#> [473] "Sox18" "Kctd4" "Nxph3" "Vat1l"
#> [477] "Cd24a" "Odf3b" "Gjb1" "Selplg"
#> [481] "Bcl11b" "Lhfp" "Ranbp3l" "Msx1"
#> [485] "Zdhhc22" "Phldb1" "Ctxn1" "Tprn"
#> [489] "Vstm2a" "Ndnf" "Pdp1" "Scn3b"
#> [493] "Cdc42ep1" "Gal3st1" "Rasd1" "Spink8"
#> [497] "Opalin" "Gja4" "Synpo2" "Pcdh20"
#> [501] "Adra1b" "Fam131a" "Tmem125" "Mb21d2"
#> [505] "Lingo3" "Ncald" "Siglech" "Rgs14"
#> [509] "Gm14964" "Gpr17" "Cx3cr1" "Ezr"
#> [513] "Adarb2" "Cpne8" "Plekhg3" "Lamb2"
#> [517] "Creb5" "Cntn2" "Aldh1a1" "Phgdh"
#> [521] "Tnfaip6" "Camk2d" "Shisa6" "Cthrc1"
#> [525] "Tmem119" "Hmgb2" "Tmem158" "Dsp"
#> [529] "Lrtm2" "Gabra5" "Tns1" "Nell1"
#> [533] "Slain1" "Prr18" "S100a8" "S100a9"
#> [537] "Col8a2" "Synpr" "Sertm1" "Adgrf5"
#> [541] "Capg" "Gjc3" "Fcer1g" "Pde1a"
#> [545] "Tafa1" "Ddn" "Hopx" "Ptk2b"
#> [549] "Rgs3" "Kcng2" "Ntng1" "H2-Q7"
#> [553] "Ifitm2" "Plaat3" "Plekhh1" "Myl4"
#> [557] "H2-K1" "Dpp6" "Tmem91" "Cyp2d22"
#> [561] "Ttr" "Suclg2" "Patj" "Btbd3"
#> [565] "Unc13c" "Syt9" "Shisal1" "Grm4"
#> [569] "Sox11" "Slc22a8" "Slc24a3" "Klk8"
#> [573] "Ipcef1" "Tnnt1" "Hhip" "Spag8"
#> [577] "Fxyd6" "Ppp1r3c" "Cbln4" "Nnat"
#> [581] "Myl9" "Vxn" "Lgals1" "Gpr88"
#> [585] "Ctxn3" "Lyz2" "Tmem100" "Wfdc17"
#> [589] "Ahnak" "Hba-a2" "Hba-a1" "Ccdc153"
#> [593] "Ccnd1" "Serpinh1" "Gad1" "Arhgef10"
#> [597] "2410004P03Rik" "Nt5dc2" "Cebpd" "Sod3"
#> [601] "H2-D1" "C4b" "Tmem88b" "Hbb-bt"
#> [605] "Rhog" "Rprm" "Ly6a" "Mog"
#> [609] "Trbc2" "Igkc" "Smim1" "Hs3st4"
#> [613] "Evi2a" "Prkcg" "Ly6c1" "Gbp4"
#> [617] "Wipf3" "BC039966" "Gm13889" "Plcxd2"
#> [621] "Mia" "Pou3f1" "Lrrc10b" "Apol11b"
#> [625] "Gpr62" "Shisa8" "Gm2115" "Kctd12"
#> [629] "1700047M11Rik" "Lhfpl3" "C030029H02Rik" "Gm19935"
#> [633] "9630013A20Rik" "2900040C04Rik"
#>
#> $cor_hclust
#> list()
#>
#> $cor_clusters
#> list()
#>
#> attr(,"class")
#> [1] "spatCorObject" "list"
# This analysis can also be performed with data outside of the gobject
detectSpatialCorFeatsMatrix(
expression_matrix = getExpression(
g,
output = "matrix"
),
method = "network",
spatial_network = getSpatialNetwork(g, output = "networkDT")
)
#> $cor_DT
#> feat_ID variable spat_cor expr_cor cordiff spatrank
#> <char> <fctr> <num> <num> <num> <int>
#> 1: 1110017D15Rik 1110017D15Rik 1.0000000 1.00000000 0.00000000 1
#> 2: 1110017D15Rik Dynlrb2 0.9071450 0.84973343 0.05741162 2
#> 3: 1110017D15Rik Ccdc153 0.9054963 0.84504575 0.06045057 3
#> 4: 1110017D15Rik Tmem212 0.9024137 0.81451232 0.08790135 4
#> 5: 1110017D15Rik Cfap126 0.8814460 0.77851057 0.10293547 5
#> ---
#> 401952: Zmat4 Thbs4 -0.1808436 -0.08644981 -0.09439376 630
#> 401953: Zmat4 Mal -0.1814648 -0.10522798 -0.07623678 631
#> 401954: Zmat4 Fa2h -0.1874828 -0.08735847 -0.10012430 632
#> 401955: Zmat4 Gfap -0.1943739 -0.13487620 -0.05949770 633
#> 401956: Zmat4 Ninj2 -0.2061581 -0.11224072 -0.09391739 634
#> exprrank rankdiff
#> <int> <int>
#> 1: 1 0
#> 2: 2 0
#> 3: 3 0
#> 4: 4 0
#> 5: 8 -3
#> ---
#> 401952: 620 10
#> 401953: 632 -1
#> 401954: 622 10
#> 401955: 634 -1
#> 401956: 633 1
#>
#> $feat_order
#> [1] "Gna12" "Ccnd2" "Btbd17" "Sox9"
#> [5] "Sez6" "Serpinf1" "S100a6" "Col1a1"
#> [9] "Vwf" "Esam" "Npas1" "Tiam1"
#> [13] "Bcam" "Hmgn2" "Rab3b" "Inmt"
#> [17] "Ddr1" "Homer3" "Cp" "Calb2"
#> [21] "Man1a" "Efnb3" "Hlf" "Gstm7"
#> [25] "Cavin1" "Sst" "Hapln2" "Hspb1"
#> [29] "Ndrg1" "Nid1" "Kit" "Pvalb"
#> [33] "Tmbim1" "Crip1" "Tek" "Elovl1"
#> [37] "Cyba" "Itih3" "Cnp" "Hap1"
#> [41] "Clic1" "Stx1a" "Arpp19" "Dio2"
#> [45] "Id3" "Crlf1" "Ttc9b" "Carhsp1"
#> [49] "Cabp7" "Fam163b" "Rarres2" "Syn2"
#> [53] "Ick" "Prox1" "Adssl1" "Vipr2"
#> [57] "Gltp" "Amotl1" "Bcas1" "Aldh1a2"
#> [61] "Tppp3" "Sirt2" "Lpl" "Cers2"
#> [65] "Qdpr" "Stk32c" "Lbp" "Hsd11b1"
#> [69] "Vtn" "Stac2" "Plxdc1" "Igfbp4"
#> [73] "Dbndd2" "Pltp" "Slc12a4" "Cadps2"
#> [77] "Erbb3" "Pmp22" "Kcnab3" "Myh11"
#> [81] "Plod1" "Etnppl" "Arhgef25" "Rcn3"
#> [85] "Vip" "Utrn" "Grm1" "Reep3"
#> [89] "Fabp7" "Dcn" "Slc17a8" "Dusp6"
#> [93] "Kitl" "Ccn2" "Timp3" "Ascl1"
#> [97] "Unc5b" "Vsir" "Gamt" "Ptprb"
#> [101] "Csrp2" "Adarb1" "Rnf130" "Nefh"
#> [105] "Aebp1" "Sept4" "Gria1" "Sypl"
#> [109] "Arsg" "Cacng4" "Rab37" "Itgb4"
#> [113] "Aspa" "Cygb" "Rflnb" "Doc2b"
#> [117] "Gfap" "Npas3" "Serpina3n" "Clmn"
#> [121] "Prkch" "Fbln5" "Akr1c18" "Gng4"
#> [125] "Sema4d" "Cxcl14" "Hexb" "Iqgap2"
#> [129] "Crhbp" "Rab3c" "Thbs4" "Serinc5"
#> [133] "Erbin" "Prkcd" "Pdlim2" "Ednrb"
#> [137] "Cpne6" "Sema5a" "Matn2" "Nptxr"
#> [141] "Enpp2" "Efcab6" "Ppp1r1a" "Litaf"
#> [145] "Il1rap" "Apod" "Cpox" "Grik1"
#> [149] "Clic6" "Nr4a1" "Igfbp6" "Sncg"
#> [153] "Gzma" "Grm2" "Prph" "Rsph1"
#> [157] "Sox8" "Fam234a" "Lims2" "Aqp4"
#> [161] "Slc12a2" "Cd74" "Pdgfrb" "Csf1r"
#> [165] "Cbln2" "Frmd8" "Gldc" "Tcf7l2"
#> [169] "Bhlhe22" "Kcnip2" "Alas2" "Gdf11"
#> [173] "Baiap2" "Ifitm3" "Phkg1" "Nptx1"
#> [177] "Pde8a" "Itih5" "Homer2" "Fam20c"
#> [181] "Cplx2" "Myo5b" "Snca" "Col3a1"
#> [185] "Ecrg4" "Map4k4" "2010300C02Rik" "Ogfrl1"
#> [189] "Fn1" "Efhd1" "Ngef" "Bok"
#> [193] "Tmem163" "Lct" "Cfh" "Ptpn4"
#> [197] "Tnni1" "Csrp1" "Nfasc" "Syt2"
#> [201] "Atp2b4" "Rgs16" "Ncf2" "Cnih3"
#> [205] "Tmem63a" "Cfap126" "Meig1" "Ccdc3"
#> [209] "Rgs5" "Enkur" "Myoc" "Vim"
#> [213] "Prkcq" "Gad2" "Lcn2" "Nr4a2"
#> [217] "Ermn" "Fibcd1" "Gsn" "Grb14"
#> [221] "Notch1" "Ube2l6" "Gatm" "Cd82"
#> [225] "Mdk" "Lamp5" "Itpka" "Chgb"
#> [229] "Mal" "Pdyn" "Nkx2-2" "Edn3"
#> [233] "Car2" "Col9a3" "Chrna4" "Gss"
#> [237] "Slc7a11" "Tm4sf1" "Kcnab1" "Shox2"
#> [241] "Serpini1" "Tspan2" "S100a11" "Vcam1"
#> [245] "Lef1" "Npy2r" "F3" "Calb1"
#> [249] "Epha7" "Slc44a1" "1110017D15Rik" "Tpm2"
#> [253] "Slc6a9" "Laptm5" "Sema3c" "Hpca"
#> [257] "Padi2" "Slc4a2" "Gabrd" "Rgs12"
#> [261] "Slc30a3" "Emilin1" "1700001C02Rik" "Gabra4"
#> [265] "Pdgfra" "Epha5" "Tesc" "Pitpnm2"
#> [269] "Mmp17" "Cit" "Foxp2" "Arpc1b"
#> [273] "Col1a2" "Eln" "Pcolce" "Tsc22d4"
#> [277] "Cald1" "Ccdc136" "Npy" "Slc13a4"
#> [281] "Gkn3" "Slc6a13" "Mgp" "Lmo3"
#> [285] "Slco1c1" "Cpne9" "Itpr2" "Slc6a11"
#> [289] "Vamp1" "Cd9" "Pglyrp1" "Slc17a6"
#> [293] "Sipa1l3" "Sh3gl3" "Plekhb1" "Nupr1"
#> [297] "Dkk3" "Cox6a2" "Dkkl1" "Fgfr2"
#> [301] "Crym" "Slc38a5" "Flna" "Bgn"
#> [305] "Col4a1" "Plat" "Nr3c2" "Cbln1"
#> [309] "Gab1" "Pllp" "Necab2" "Dbndd1"
#> [313] "Agt" "Cryab" "Tagln" "Mcam"
#> [317] "Olfm2" "Icam5" "Anxa2" "Rora"
#> [321] "Calml4" "Htr3a" "Paqr5" "Rasgrf1"
#> [325] "Zic1" "Mobp" "Hhatl" "Trf"
#> [329] "Cpne4" "Cdhr4" "Cd59a" "Gng11"
#> [333] "Chrm1" "Prr5l" "Ugt8a" "Rims3"
#> [337] "Sgpp2" "Camkv" "Sox10" "Micall1"
#> [341] "Tie1" "Fa2h" "Ucp2" "Vav3"
#> [345] "Ccp110" "Gria2" "Rasl10a" "Foxj1"
#> [349] "Trim59" "Dynlrb2" "Gjc1" "Neurod1"
#> [353] "Ttyh2" "Cpne7" "Nrip3" "Tbr1"
#> [357] "Lcat" "Tmem98" "Myo1d" "Prdm8"
#> [361] "Tgfbi" "Kcnc2" "Thrsp" "Isg15"
#> [365] "Acta2" "H2-Q4" "Dock4" "Myrf"
#> [369] "Lmo1" "Igfbp7" "P2ry12" "Pcdh8"
#> [373] "Lgi4" "Fxyd1" "Fxyd7" "Mag"
#> [377] "Zcchc12" "Anln" "Wnt4" "C1ql2"
#> [381] "Unc93b1" "Tspan15" "Ppp1r14a" "Clic4"
#> [385] "Galnt6" "Ccn3" "Rims2" "Zmat4"
#> [389] "Cldn11" "Ccdc33" "Slc32a1" "Tgm2"
#> [393] "Vstm2l" "Neurod6" "Crygn" "Enpp6"
#> [397] "Neurod2" "Satb2" "Pcp4l1" "Txnip"
#> [401] "Egr1" "Otud7b" "Car14" "Rgs4"
#> [405] "Dock10" "Lpar1" "Trps1" "Ptpn3"
#> [409] "Lefty1" "Zfhx3" "St6galnac5" "Ak5"
#> [413] "Hrh3" "Nexn" "Adgrl4" "Rlbp1"
#> [417] "Igfbp2" "Wfs1" "Cplx3" "Orai2"
#> [421] "Olig2" "Gpr37" "Plcb4" "Nxph4"
#> [425] "Ndufa4l2" "Cacng5" "Plekhg1" "Cmtm5"
#> [429] "Gpr161" "Rfx3" "Igsf21" "Ramp3"
#> [433] "Arhgap12" "Nkx6-2" "Ninj2" "Cldn5"
#> [437] "Htr2c" "Hspb8" "Fmod" "Prelp"
#> [441] "Mpped1" "Rapgef5" "Vwa1" "Stab1"
#> [445] "Arl15" "Reln" "Mustn1" "Pbxip1"
#> [449] "Dnali1" "Id1" "Lrrtm3" "Tmem212"
#> [453] "Epop" "Gjc2" "1190005I06Rik" "Ctla2a"
#> [457] "Cnr1" "Gpr4" "Sowaha" "Tent5c"
#> [461] "Serpinb1a" "S1pr5" "Penk" "Cdc42ep2"
#> [465] "Slitrk6" "Hpcal4" "Olig1" "Rprml"
#> [469] "Stxbp6" "Hs3st2" "Rbp1" "Ppm1e"
#> [473] "Sox18" "Kctd4" "Nxph3" "Vat1l"
#> [477] "Cd24a" "Odf3b" "Gjb1" "Selplg"
#> [481] "Bcl11b" "Lhfp" "Ranbp3l" "Msx1"
#> [485] "Zdhhc22" "Phldb1" "Ctxn1" "Tprn"
#> [489] "Vstm2a" "Ndnf" "Pdp1" "Scn3b"
#> [493] "Cdc42ep1" "Gal3st1" "Rasd1" "Spink8"
#> [497] "Opalin" "Gja4" "Synpo2" "Pcdh20"
#> [501] "Adra1b" "Fam131a" "Tmem125" "Mb21d2"
#> [505] "Lingo3" "Ncald" "Siglech" "Rgs14"
#> [509] "Gm14964" "Gpr17" "Cx3cr1" "Ezr"
#> [513] "Adarb2" "Cpne8" "Plekhg3" "Lamb2"
#> [517] "Creb5" "Cntn2" "Aldh1a1" "Phgdh"
#> [521] "Tnfaip6" "Camk2d" "Shisa6" "Cthrc1"
#> [525] "Tmem119" "Hmgb2" "Tmem158" "Dsp"
#> [529] "Lrtm2" "Gabra5" "Tns1" "Nell1"
#> [533] "Slain1" "Prr18" "S100a8" "S100a9"
#> [537] "Col8a2" "Synpr" "Sertm1" "Adgrf5"
#> [541] "Capg" "Gjc3" "Fcer1g" "Pde1a"
#> [545] "Tafa1" "Ddn" "Hopx" "Ptk2b"
#> [549] "Rgs3" "Kcng2" "Ntng1" "H2-Q7"
#> [553] "Ifitm2" "Plaat3" "Plekhh1" "Myl4"
#> [557] "H2-K1" "Dpp6" "Tmem91" "Cyp2d22"
#> [561] "Ttr" "Suclg2" "Patj" "Btbd3"
#> [565] "Unc13c" "Syt9" "Shisal1" "Grm4"
#> [569] "Sox11" "Slc22a8" "Slc24a3" "Klk8"
#> [573] "Ipcef1" "Tnnt1" "Hhip" "Spag8"
#> [577] "Fxyd6" "Ppp1r3c" "Cbln4" "Nnat"
#> [581] "Myl9" "Vxn" "Lgals1" "Gpr88"
#> [585] "Ctxn3" "Lyz2" "Tmem100" "Wfdc17"
#> [589] "Ahnak" "Hba-a2" "Hba-a1" "Ccdc153"
#> [593] "Ccnd1" "Serpinh1" "Gad1" "Arhgef10"
#> [597] "2410004P03Rik" "Nt5dc2" "Cebpd" "Sod3"
#> [601] "H2-D1" "C4b" "Tmem88b" "Hbb-bt"
#> [605] "Rhog" "Rprm" "Ly6a" "Mog"
#> [609] "Trbc2" "Igkc" "Smim1" "Hs3st4"
#> [613] "Evi2a" "Prkcg" "Ly6c1" "Gbp4"
#> [617] "Wipf3" "BC039966" "Gm13889" "Plcxd2"
#> [621] "Mia" "Pou3f1" "Lrrc10b" "Apol11b"
#> [625] "Gpr62" "Shisa8" "Gm2115" "Kctd12"
#> [629] "1700047M11Rik" "Lhfpl3" "C030029H02Rik" "Gm19935"
#> [633] "9630013A20Rik" "2900040C04Rik"
#>
#> $cor_hclust
#> list()
#>
#> $cor_clusters
#> list()
#>
#> attr(,"class")
#> [1] "list" "spatCorObject"