Skip to contents

Projection Plot

Source: R/ProjectionPlot.R
ProjectionPlot.Rd

This function generates a projection plot, which can be used to compare two groups of cells in a dimensionality reduction space.

Usage

ProjectionPlot(
  srt_query,
  srt_ref,
  query_group = NULL,
  ref_group = NULL,
  query_reduction = "ref.embeddings",
  ref_reduction = srt_query[[query_reduction]]@misc[["reduction.model"]] %||% NULL,
  query_param = list(palette = "Set1", cells.highlight = TRUE),
  ref_param = list(palette = "Paired"),
  xlim = NULL,
  ylim = NULL,
  pt.size = 0.8,
  stroke.highlight = 0.5
)

Arguments

srt_query

A Seurat object storing the query cells.

srt_ref

A Seurat object storing the reference cells.

query_group

The grouping variable for the query group cells.

ref_group

The grouping variable for the reference group cells.

query_reduction

The name of the reduction in the query group cells.

ref_reduction

The name of the reduction in the reference group cells.

query_param

A list of parameters for customizing the query group plot. Available parameters: palette (color palette for groups) and cells.highlight (whether to highlight cells).

ref_param

A list of parameters for customizing the reference group plot. Available parameters: palette (color palette for groups) and cells.highlight (whether to highlight cells).

xlim

The x-axis limits for the plot. If not provided, the limits will be calculated based on the data.

ylim

The y-axis limits for the plot. If not provided, the limits will be calculated based on the data.

pt.size

The size of the points in the plot.

stroke.highlight

The size of the stroke highlight for cells.

Examples

data(panc8_sub)
panc8_sub <- standard_scop(panc8_sub)
#> ℹ [2026-01-27 07:51:55] Start standard scop workflow...
#> ℹ [2026-01-27 07:51:56] Checking a list of <Seurat>...
#> ! [2026-01-27 07:51:56] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-01-27 07:51:56] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on the data 1/1 of the `srt_list`...
#> ℹ [2026-01-27 07:51:58] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2026-01-27 07:51:59] Use the separate HVF from srt_list
#> ℹ [2026-01-27 07:51:59] Number of available HVF: 2000
#> ℹ [2026-01-27 07:51:59] Finished check
#> ℹ [2026-01-27 07:51:59] Perform `Seurat::ScaleData()`
#> ℹ [2026-01-27 07:52:00] Perform pca linear dimension reduction
#> ℹ [2026-01-27 07:52:01] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-01-27 07:52:01] Reorder clusters...
#> ℹ [2026-01-27 07:52:01] Perform umap nonlinear dimension reduction
#> ℹ [2026-01-27 07:52:01] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2026-01-27 07:52:06] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ✔ [2026-01-27 07:52:10] Run scop standard workflow completed
srt_ref <- panc8_sub[, panc8_sub$tech != "fluidigmc1"]
srt_query <- panc8_sub[, panc8_sub$tech == "fluidigmc1"]
srt_ref <- integration_scop(
  srt_ref,
  batch = "tech",
  integration_method = "Uncorrected"
)
#> ◌ [2026-01-27 07:52:10] Run Uncorrected integration...
#> ℹ [2026-01-27 07:52:10] Spliting `srt_merge` into `srt_list` by column "tech"...
#> ℹ [2026-01-27 07:52:11] Checking a list of <Seurat>...
#> ℹ [2026-01-27 07:52:11] Data 1/4 of the `srt_list` has been log-normalized
#> ℹ [2026-01-27 07:52:11] Perform `Seurat::FindVariableFeatures()` on the data 1/4 of the `srt_list`...
#> ℹ [2026-01-27 07:52:12] Data 2/4 of the `srt_list` has been log-normalized
#> ℹ [2026-01-27 07:52:12] Perform `Seurat::FindVariableFeatures()` on the data 2/4 of the `srt_list`...
#> ℹ [2026-01-27 07:52:12] Data 3/4 of the `srt_list` has been log-normalized
#> ℹ [2026-01-27 07:52:12] Perform `Seurat::FindVariableFeatures()` on the data 3/4 of the `srt_list`...
#> ℹ [2026-01-27 07:52:13] Data 4/4 of the `srt_list` has been log-normalized
#> ℹ [2026-01-27 07:52:13] Perform `Seurat::FindVariableFeatures()` on the data 4/4 of the `srt_list`...
#> ℹ [2026-01-27 07:52:13] Use the separate HVF from srt_list
#> ℹ [2026-01-27 07:52:14] Number of available HVF: 2000
#> ℹ [2026-01-27 07:52:14] Finished check
#> ℹ [2026-01-27 07:52:15] Perform Uncorrected integration
#> ℹ [2026-01-27 07:52:16] Perform `Seurat::ScaleData()`
#> ℹ [2026-01-27 07:52:16] Perform linear dimension reduction("pca")
#> ℹ [2026-01-27 07:52:18] Perform Seurat::FindClusters ("louvain")
#> ℹ [2026-01-27 07:52:18] Reorder clusters...
#> ℹ [2026-01-27 07:52:18] Perform nonlinear dimension reduction ("umap")
#> ℹ [2026-01-27 07:52:18] Non-linear dimensionality reduction (umap) using (Uncorrectedpca) dims (1-10) as input
#> ℹ [2026-01-27 07:52:22] Non-linear dimensionality reduction (umap) using (Uncorrectedpca) dims (1-10) as input
#> ✔ [2026-01-27 07:52:27] Run Uncorrected integration done
CellDimPlot(
  srt_ref,
  group.by = c("celltype", "tech")
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.


# Projection
srt_query <- RunKNNMap(
  srt_query = srt_query,
  srt_ref = srt_ref,
  ref_umap = "UncorrectedUMAP2D"
)
#> ℹ [2026-01-27 07:52:28] Use the features to calculate distance metric
#> ℹ [2026-01-27 07:52:29] Data type is log-normalized
#> Warning: The following features were labelled as variable in 'var.features' but had no corresponding rank in `var.features.rank` and will therefore be ignored: 'A4GALT', 'AADAC', 'AARS2', 'ABCA1', 'ABCC3', 'ABCC4', 'ABCC8', 'ABCC9', 'ABCG2', 'ABHD15', 'ABI3', 'ABL2', 'ABTB2', 'ACACB', 'ACBD7', 'ACE', 'ACHE', 'ACSL3', 'ACSL4', 'ACTG1', 'ACTN1', 'ACTN4', 'ADAM12', 'ADAM9', 'ADAMTS1', 'ADAMTS2', 'ADAMTSL2', 'ADAT1', 'ADCK3', 'ADCY1', 'ADCY3', 'ADCY5', 'ADD3', 'ADM', 'ADRA2A', 'ADRA2C', 'ADRB1', 'ADRBK2', 'AFAP1L2', 'AGR2', 'AGRN', 'AHR', 'AIFM3', 'AIM1L', 'AIM1', 'AJAP1', 'AK5', 'AKAP7', 'ALDH1A1', 'ALDH1A2', 'ALDH2', 'ALDH3A2', 'ALDH3B1', 'ALDH4A1', 'ALOX5AP', 'ALPL', 'AMOTL1', 'AMOTL2', 'ANGPTL1', 'ANO6', 'ANO9', 'ANTXR2', 'AOC2', 'AP1S2', 'AP1S3', 'APOBEC2', 'APOD', 'AQP3', 'AQP4', 'ARHGAP26', 'ARHGAP29', 'ARHGAP6', 'ARHGEF17', 'ARHGEF2', 'ARHGEF3', 'ARHGEF40', 'ARHGEF6', 'ARL14', 'ARL4D', 'ARL6', 'ARMC9', 'ARNTL2', 'ARSJ', 'ARX', 'ASAP1', 'ASCL1', 'ASNS', 'ASPH', 'ASRGL1', 'ASS1', 'ASTN2', 'ASXL3', 'ATCAY', 'ATF3', 'ATF5', 'ATHL1', 'ATP10B', 'ATP11A', 'ATP1A1', 'ATP1B2', 'ATP2A3', 'ATP2B4', 'ATP8B1', 'AURKB', 'B3GNT2', 'B4GALT1', 'B4GALT5', 'BACE2', 'BACH2', 'BAIAP2L1', 'BAIAP3', 'BAMBI', 'BARX2', 'BASP1', 'BATF', 'BAZ1A', 'BBC3', 'BCHE', 'BCL2L15', 'BCL3', 'BCL6B', 'BCL6', 'BDH2', 'BHLHE41', 'BHMT2', 'BIK', 'BIRC5', 'BMF', 'BMP2', 'BMPR2', 'BNC2', 'BRIP1', 'BUB1', 'C1QL1', 'C1QTNF1', 'C1RL', 'C2CD4A', 'C2CD4B', 'CABP4', 'CACNA2D1', 'CADM2', 'CADPS2', 'CALCA', 'CALML4', 'CALU', 'CALY', 'CAMK1D', 'CAMKK1', 'CAMKK2', 'CAPN5', 'CAPN6', 'CARHSP1', 'CARTPT', 'CASP6', 'CAV2', 'CBR1', 'CCDC15', 'CCDC71L', 'CCL28', 'CCND2', 'CCNF', 'CCNG2', 'CD200', 'CD276', 'CD47', 'CD68', 'CD82', 'CDCA3', 'CDH17', 'CDH1', 'CDH23', 'CDH2', 'CDH3', 'CDHR2', 'CDK17', 'CDKN1A', 'CDKN2A', 'CDKN2B', 'CDR2', 'CDT1', 'CDX2', 'CEACAM1', 'CEBPB', 'CELF2', 'CENPF', 'CENPW', 'CERCAM', 'CFI', 'CFLAR', 'CGN', 'CHAC1', 'CHGB', 'CHN2', 'CHRM3', 'CHST1', 'CHSY1', 'CITED2', 'CITED4', 'CLCF1', 'CLCN4', 'CLDN11', 'CLDN19', 'CLDN3', 'CLDN5', 'CLDN6', 'CLDN7', 'CLEC11A', 'CLIC5', 'CLIC6', 'CLMN', 'CLMP', 'CLRN3', 'CLSPN', 'CMPK2', 'CMTM3', 'CMTM7', 'CNIH2', 'CNN2', 'CNN3', 'CNNM1', 'CNTN1', 'COCH', 'COL13A1', 'COL14A1', 'COL16A1', 'COL18A1', 'COL5A3', 'COL9A2', 'COMMD2', 'COMP', 'CORO1C', 'CORO2A', 'COX7A1', 'CPA3', 'CPLX2', 'CPM', 'CRABP2', 'CRADD', 'CREB3L1', 'CREB5', 'CREG2', 'CRIP1', 'CRLF1', 'CRTAC1', 'CRTAP', 'CTHRC1', 'CTNNA2', 'CTSB', 'CTSC', 'CTSS', 'CX3CL1', 'CXADR', 'CXCL12', 'CXCL16', 'CYB5A', 'CYBRD1', 'CYP20A1', 'CYP27B1', 'CYR61', 'CYTH3', 'DAB2IP', 'DACH1', 'DACT1', 'DAG1', 'DBN1', 'DCAF11', 'DCBLD2', 'DCUN1D2', 'DDAH2', 'DDC', 'DDIT3', 'DDX25', 'DDX51', 'DGKA', 'DHCR7', 'DHDH', 'DHODH', 'DHRS2', 'DIXDC1', 'DKK1', 'DMBT1', 'DMC1', 'DNAJB9', 'DNAJC22', 'DNER', 'DOCK4', 'DOCK5', 'DOK5', 'DPEP1', 'DPP9', 'DRAM1', 'DSC2', 'DSG2', 'DTNA', 'DUSP10', 'DUSP14', 'DUSP1', 'DUSP23', 'DUSP2', 'DUSP5', 'DZANK1', 'EBP', 'ECE1', 'ECEL1', 'EDN2', 'EFCAB7', 'EFNB1', 'EFNB3', 'EGFR', 'EGF', 'EGR1', 'EGR4', 'EHD1', 'EHD4', 'EHF', 'EIF4EBP1', 'ELAVL4', 'EMILIN1', 'EMP2', 'ENAH', 'ENG', 'ENPP2', 'EPAS1', 'EPDR1', 'EPHA2', 'EPHB2', 'EPHX1', 'EPS8L1', 'ERBB2', 'ERBB3', 'ERO1LB', 'ERO1L', 'ERRFI1', 'ESRRG', 'ETS2', 'ETV1', 'EVA1B', 'EVC2', 'EXT1', 'F10', 'F11R', 'F2RL1', 'F5', 'FA2H', 'FABP5', 'FADS1', 'FADS2', 'FAM101B', 'FAM105A', 'FAM107B', 'FAM129B', 'FAM134B', 'FAM155A', 'FAM159B', 'FAM161A', 'FAM162A', 'FAM163A', 'FAM20C', 'FAM217B', 'FAM227A', 'FAM43A', 'FAM46B', 'FAM46C', 'FAM73A', 'FAM84A', 'FAM84B', 'FBLIM1', 'FBLN1', 'FBLN5', 'FBP1', 'FBXL18', 'FBXO2', 'FBXO6', 'FCER1G', 'FDFT1', 'FERMT2', 'FEV', 'FEZ1', 'FFAR2', 'FFAR4', 'FGD2', 'FGD4', 'FGF7', 'FGFBP1', 'FGFR2', 'FGFR3', 'FGL2', 'FHL2', 'FKBP10', 'FKBP11', 'FKBP5', 'FLNA', 'FNDC4', 'FOLR1', 'FOSB', 'FOSL2', 'FOXC1', 'FOXM1', 'FOXQ1', 'FRAS1', 'FRMD4B', 'FSCN1', 'FXN', 'FXYD3', 'FXYD5', 'FXYD6', 'FZD5', 'G0S2', 'GAD2', 'GADD45A', 'GADD45B', 'GADD45G', 'GALE', 'GALM', 'GALNT2', 'GALNT3', 'GAL', 'GAS6', 'GAS7', 'GATA2', 'GCK', 'GCLC', 'GCNT1', 'GC', 'GDPD1', 'GFOD2', 'GFRA1', 'GGT1', 'GGT5', 'GHR', 'GINS3', 'GINS4', 'GJA1', 'GJA4', 'GJB1', 'GJB3', 'GJC1', 'GK5', 'GK', 'GLDC', 'GLI2', 'GLIPR2', 'GLT1D1', 'GLUL', 'GMDS', 'GMEB1', 'GMFG', 'GMNN', 'GNAL', 'GNPNAT1', 'GNPTAB', 'GOLM1', 'GOT1', 'GPC1', 'GPC6', 'GPR155', 'GPR160', 'GPR161', 'GPR4', 'GPRC5A', 'GPRC5B', 'GPSM1', 'GPT2', 'GPX3', 'GREB1', 'GSN', 'GSTM3', 'GSTM5', 'GSTP1', 'GTF2A1', 'GTPBP10', 'GUCA1B', 'GUCA2A', 'GUCY1A3', 'GULP1', 'GYLTL1B', 'H19', 'HABP2', 'HAP1', 'HBEGF', 'HCK', 'HDHD3', 'HEATR5A', 'HEBP1', 'HEG1', 'HEPH', 'HERPUD1', 'HES1', 'HIC1', 'HIF1A', 'HILPDA', 'HIP1', 'HIRA', 'HIST1H1C', 'HIST1H2BK', 'HIST2H2BE', 'HK1', 'HK2', 'HKDC1', 'HMGB3', 'HMGCS1', 'HMGN5', 'HMOX1', 'HN1', 'HNF1B', 'HNF4A', 'HNMT', 'HOMER2', 'HOPX', 'HOXB2', 'HOXB4', 'HPCAL1', 'HPGD', 'HPN', 'HS3ST1', 'HS3ST3A1', 'HS6ST2', 'HSD11B2', 'HSD17B11', 'HSPA1A', 'HSPA1B', 'HSPA5', 'HSPB6', 'HSPB8', 'HTRA1', 'HUNK', 'HYAL3', 'IBA57', 'ID1', 'ID4', 'IDH1', 'IDH2', 'IER2', 'IER3', 'IFI30', 'IFIT1', 'IFITM2', 'IFNGR1', 'IGFBP6', 'IGFBPL1', 'IGSF3', 'IKBIP', 'IKBKE', 'IKZF3', 'IL11', 'IL15RA', 'IL1RN', 'IL22RA1', 'IL33', 'IMPA2', 'INHBB', 'INPP4B', 'INSIG1', 'INSM1', 'IQGAP2', 'IRAK2', 'IRF1', 'IRS2', 'IRX1', 'IRX2', 'ISG20', 'ISL1', 'ITGA11', 'ITGA1', 'ITGA3', 'ITGA6', 'ITGAV', 'ITGB1', 'ITGB4', 'ITGB8', 'ITIH5', 'ITPR2', 'IVNS1ABP', 'IYD', 'JAM3', 'JARID2', 'JDP2', 'JMJD6', 'JPX', 'JUNB', 'JUN', 'JUP', 'KCNA5', 'KCNE3', 'KCNG1', 'KCNH6', 'KCNJ13', 'KCNJ5', 'KCNJ6', 'KCNJ8', 'KCNK16', 'KCNK5', 'KCNN2', 'KCNN3', 'KCNQ1OT1', 'KCNQ1', 'KCTD12', 'KDELC2', 'KDELR3', 'KIF11', 'KIF12', 'KIF20B', 'KIF21B', 'KIF5C', 'KIT', 'KLB', 'KLF2', 'KLF4', 'KLF5', 'KLF6', 'KLF7', 'KLHL28', 'KLHL31', 'KLHL3', 'KLK10', 'KLK11', 'KREMEN1', 'KRT15', 'KRT17', 'KRTCAP3', 'KYNU', 'L1TD1', 'L2HGDH', 'LAD1', 'LAIR1', 'LAMA1', 'LAMA3', 'LAMB1', 'LAMB2', 'LAMB3', 'LARP6', 'LASP1', 'LBH', 'LCP1', 'LDB2', 'LDLR', 'LEFTY1', 'LFNG', 'LGALS3', 'LGALS9', 'LHFPL2', 'LIFR', 'LIF', 'LIMA1', 'LIMK2', 'LIMS1', 'LIPC', 'LIPH', 'LITAF', 'LMO1', 'LMO2', 'LMO4', 'LMO7', 'LNX2', 'LOXL1', 'LOXL2', 'LPAR1', 'LRP1', 'LRP8', 'LRRC27', 'LRRC2', 'LRRC57', 'LRRC58', 'LRRIQ1', 'LRRK2', 'LRRTM2', 'LSR', 'LSS', 'LTBP4', 'LTB', 'LTF', 'LTV1', 'LURAP1L', 'LXN', 'LY6E', 'LY6H', 'LY96', 'LYN', 'LYPD1', 'LYRM7', 'LZTS1', 'MAB21L3', 'MACC1', 'MAFB', 'MAFF', 'MAL2', 'MALL', 'MAOA', 'MAOB', 'MAP3K9', 'MAPT', 'MARCKSL1', 'MAT1A', 'MCC', 'MCL1', 'MCM2', 'MCM6', 'MCOLN2', 'MDFIC', 'MDFI', 'MDGA1', 'MDK', 'MDM1', 'ME1', 'MEDAG', 'MEF2C', 'MEIS2', 'METRNL', 'METTL21A', 'MEX3A', 'MFAP2', 'MFAP4', 'MFGE8', 'MGAT4B', 'MGLL', 'MGP', 'MICAL2', 'MID1', 'MIR143HG', 'MKNK1', 'MLLT11', 'MLXIPL', 'MMACHC', 'MMP14', 'MNS1', 'MOB3B', 'MOSPD1', 'MOXD1', 'MPPED2', 'MPST', 'MPZL2', 'MRC2', 'MS4A2', 'MSMO1', 'MSRB1', 'MSRB3', 'MSX1', 'MTHFD2', 'MTUS1', 'MVP', 'MYADM', 'MYH9', 'MYL12A', 'MYL12B', 'MYL9', 'MYLK', 'MYO1C', 'MYO5B', 'MYOF', 'MYRF', 'MYZAP', 'N4BP3', 'NAA40', 'NAP1L2', 'NCAM1', 'NCF2', 'NCMAP', 'NCS1', 'NDRG1', 'NDRG2', 'NDUFA4L2', 'NDUFA4', 'NEDD9', 'NEK6', 'NEK8', 'NEURL3', 'NEUROD1', 'NEXN', 'NFATC4', 'NFKBIE', 'NFKBIZ', 'NHSL1', 'NICN1', 'NID1', 'NID2', 'NIPSNAP3B', 'NKD1', 'NLN', 'NLRC3', 'NMB', 'NOL9', 'NOTCH1', 'NOTCH3', 'NOTCH4', 'NPHS1', 'NPR1', 'NPTX2', 'NPY1R', 'NQO1', 'NR0B1', 'NR0B2', 'NR1D1', 'NR2F2', 'NR4A2', 'NR4A3', 'NR5A2', 'NR6A1', 'NRARP', 'NREP', 'NRP2', 'NSG1', 'NT5E', 'NTM', 'NTN4', 'NUAK2', 'NUGGC', 'NUSAP1', 'NYAP2', 'OAF', 'OAS3', 'OCLN', 'ODF2L', 'OGDH', 'OLFM2', 'OLFML1', 'OLFML2B', 'ORAI2', 'ORC4', 'OSGIN1', 'OSMR', 'OVOL1', 'OXR1', 'P2RX1', 'P4HA1', 'P4HA3', 'PACSIN2', 'PAG1', 'PAH', 'PALB2', 'PAMR1', 'PANK1', 'PAQR5', 'PARD6G', 'PARM1', 'PASK', 'PCDH10', 'PCDH17', 'PCDH18', 'PCDH7', 'PCK2', 'PCP4', 'PCSK2', 'PCSK5', 'PDCD4', 'PDDC1', 'PDE1A', 'PDE3B', 'PDE4A', 'PDE4C', 'PDE7B', 'PDE8B', 'PDGFA', 'PDGFB', 'PDGFC', 'PDIA4', 'PDLIM1', 'PDLIM2', 'PDLIM3', 'PDLIM4', 'PDP1', 'PDP2', 'PDX1', 'PEAK1', 'PECAM1', 'PEG10', 'PEMT', 'PGC', 'PGM1', 'PGM2L1', 'PHGDH', 'PHGR1', 'PHLDA1', 'PHLDA2', 'PHLDA3', 'PID1', 'PIEZO1', 'PIGN', 'PIK3IP1', 'PIK3R1', 'PIM1', 'PIM2', 'PIM3', 'PIWIL2', 'PKIB', 'PLA2G15', 'PLA2G4A', 'PLA2G4C', 'PLAT', 'PLBD1', 'PLCD1', 'PLCD3', 'P
#> ℹ [2026-01-27 07:52:29] Data type is log-normalized
#> Warning: The following features were labelled as variable in 'var.features' but had no corresponding rank in `var.features.rank` and will therefore be ignored: 'A4GALT', 'AADAC', 'AARS2', 'ABCA1', 'ABCC3', 'ABCC4', 'ABCC8', 'ABCC9', 'ABCG2', 'ABHD15', 'ABI3', 'ABL2', 'ABTB2', 'ACACB', 'ACBD7', 'ACE', 'ACHE', 'ACSL3', 'ACSL4', 'ACTG1', 'ACTN1', 'ACTN4', 'ADAM12', 'ADAM9', 'ADAMTS1', 'ADAMTS2', 'ADAMTSL2', 'ADAT1', 'ADCK3', 'ADCY1', 'ADCY3', 'ADCY5', 'ADD3', 'ADM', 'ADRA2A', 'ADRA2C', 'ADRB1', 'ADRBK2', 'AFAP1L2', 'AGR2', 'AGRN', 'AHR', 'AIFM3', 'AIM1L', 'AIM1', 'AJAP1', 'AK5', 'AKAP7', 'ALDH1A1', 'ALDH1A2', 'ALDH2', 'ALDH3A2', 'ALDH3B1', 'ALDH4A1', 'ALOX5AP', 'ALPL', 'AMOTL1', 'AMOTL2', 'ANGPTL1', 'ANO6', 'ANO9', 'ANTXR2', 'AOC2', 'AP1S2', 'AP1S3', 'APOBEC2', 'APOD', 'AQP3', 'AQP4', 'ARHGAP26', 'ARHGAP29', 'ARHGAP6', 'ARHGEF17', 'ARHGEF2', 'ARHGEF3', 'ARHGEF40', 'ARHGEF6', 'ARL14', 'ARL4D', 'ARL6', 'ARMC9', 'ARNTL2', 'ARSJ', 'ARX', 'ASAP1', 'ASCL1', 'ASNS', 'ASPH', 'ASRGL1', 'ASS1', 'ASTN2', 'ASXL3', 'ATCAY', 'ATF3', 'ATF5', 'ATHL1', 'ATP10B', 'ATP11A', 'ATP1A1', 'ATP1B2', 'ATP2A3', 'ATP2B4', 'ATP8B1', 'AURKB', 'B3GNT2', 'B4GALT1', 'B4GALT5', 'BACE2', 'BACH2', 'BAIAP2L1', 'BAIAP3', 'BAMBI', 'BARX2', 'BASP1', 'BATF', 'BAZ1A', 'BBC3', 'BCHE', 'BCL2L15', 'BCL3', 'BCL6B', 'BCL6', 'BDH2', 'BHLHE41', 'BHMT2', 'BIK', 'BIRC5', 'BMF', 'BMP2', 'BMPR2', 'BNC2', 'BRIP1', 'BUB1', 'C1QL1', 'C1QTNF1', 'C1RL', 'C2CD4A', 'C2CD4B', 'CABP4', 'CACNA2D1', 'CADM2', 'CADPS2', 'CALCA', 'CALML4', 'CALU', 'CALY', 'CAMK1D', 'CAMKK1', 'CAMKK2', 'CAPN5', 'CAPN6', 'CARHSP1', 'CARTPT', 'CASP6', 'CAV2', 'CBR1', 'CCDC15', 'CCDC71L', 'CCL28', 'CCND2', 'CCNF', 'CCNG2', 'CD200', 'CD276', 'CD47', 'CD68', 'CD82', 'CDCA3', 'CDH17', 'CDH1', 'CDH23', 'CDH2', 'CDH3', 'CDHR2', 'CDK17', 'CDKN1A', 'CDKN2A', 'CDKN2B', 'CDR2', 'CDT1', 'CDX2', 'CEACAM1', 'CEBPB', 'CELF2', 'CENPF', 'CENPW', 'CERCAM', 'CFI', 'CFLAR', 'CGN', 'CHAC1', 'CHGB', 'CHN2', 'CHRM3', 'CHST1', 'CHSY1', 'CITED2', 'CITED4', 'CLCF1', 'CLCN4', 'CLDN11', 'CLDN19', 'CLDN3', 'CLDN5', 'CLDN6', 'CLDN7', 'CLEC11A', 'CLIC5', 'CLIC6', 'CLMN', 'CLMP', 'CLRN3', 'CLSPN', 'CMPK2', 'CMTM3', 'CMTM7', 'CNIH2', 'CNN2', 'CNN3', 'CNNM1', 'CNTN1', 'COCH', 'COL13A1', 'COL14A1', 'COL16A1', 'COL18A1', 'COL5A3', 'COL9A2', 'COMMD2', 'COMP', 'CORO1C', 'CORO2A', 'COX7A1', 'CPA3', 'CPLX2', 'CPM', 'CRABP2', 'CRADD', 'CREB3L1', 'CREB5', 'CREG2', 'CRIP1', 'CRLF1', 'CRTAC1', 'CRTAP', 'CTHRC1', 'CTNNA2', 'CTSB', 'CTSC', 'CTSS', 'CX3CL1', 'CXADR', 'CXCL12', 'CXCL16', 'CYB5A', 'CYBRD1', 'CYP20A1', 'CYP27B1', 'CYR61', 'CYTH3', 'DAB2IP', 'DACH1', 'DACT1', 'DAG1', 'DBN1', 'DCAF11', 'DCBLD2', 'DCUN1D2', 'DDAH2', 'DDC', 'DDIT3', 'DDX25', 'DDX51', 'DGKA', 'DHCR7', 'DHDH', 'DHODH', 'DHRS2', 'DIXDC1', 'DKK1', 'DMBT1', 'DMC1', 'DNAJB9', 'DNAJC22', 'DNER', 'DOCK4', 'DOCK5', 'DOK5', 'DPEP1', 'DPP9', 'DRAM1', 'DSC2', 'DSG2', 'DTNA', 'DUSP10', 'DUSP14', 'DUSP1', 'DUSP23', 'DUSP2', 'DUSP5', 'DZANK1', 'EBP', 'ECE1', 'ECEL1', 'EDN2', 'EFCAB7', 'EFNB1', 'EFNB3', 'EGFR', 'EGF', 'EGR1', 'EGR4', 'EHD1', 'EHD4', 'EHF', 'EIF4EBP1', 'ELAVL4', 'EMILIN1', 'EMP2', 'ENAH', 'ENG', 'ENPP2', 'EPAS1', 'EPDR1', 'EPHA2', 'EPHB2', 'EPHX1', 'EPS8L1', 'ERBB2', 'ERBB3', 'ERO1LB', 'ERO1L', 'ERRFI1', 'ESRRG', 'ETS2', 'ETV1', 'EVA1B', 'EVC2', 'EXT1', 'F10', 'F11R', 'F2RL1', 'F5', 'FA2H', 'FABP5', 'FADS1', 'FADS2', 'FAM101B', 'FAM105A', 'FAM107B', 'FAM129B', 'FAM134B', 'FAM155A', 'FAM159B', 'FAM161A', 'FAM162A', 'FAM163A', 'FAM20C', 'FAM217B', 'FAM227A', 'FAM43A', 'FAM46B', 'FAM46C', 'FAM73A', 'FAM84A', 'FAM84B', 'FBLIM1', 'FBLN1', 'FBLN5', 'FBP1', 'FBXL18', 'FBXO2', 'FBXO6', 'FCER1G', 'FDFT1', 'FERMT2', 'FEV', 'FEZ1', 'FFAR2', 'FFAR4', 'FGD2', 'FGD4', 'FGF7', 'FGFBP1', 'FGFR2', 'FGFR3', 'FGL2', 'FHL2', 'FKBP10', 'FKBP11', 'FKBP5', 'FLNA', 'FNDC4', 'FOLR1', 'FOSB', 'FOSL2', 'FOXC1', 'FOXM1', 'FOXQ1', 'FRAS1', 'FRMD4B', 'FSCN1', 'FXN', 'FXYD3', 'FXYD5', 'FXYD6', 'FZD5', 'G0S2', 'GAD2', 'GADD45A', 'GADD45B', 'GADD45G', 'GALE', 'GALM', 'GALNT2', 'GALNT3', 'GAL', 'GAS6', 'GAS7', 'GATA2', 'GCK', 'GCLC', 'GCNT1', 'GC', 'GDPD1', 'GFOD2', 'GFRA1', 'GGT1', 'GGT5', 'GHR', 'GINS3', 'GINS4', 'GJA1', 'GJA4', 'GJB1', 'GJB3', 'GJC1', 'GK5', 'GK', 'GLDC', 'GLI2', 'GLIPR2', 'GLT1D1', 'GLUL', 'GMDS', 'GMEB1', 'GMFG', 'GMNN', 'GNAL', 'GNPNAT1', 'GNPTAB', 'GOLM1', 'GOT1', 'GPC1', 'GPC6', 'GPR155', 'GPR160', 'GPR161', 'GPR4', 'GPRC5A', 'GPRC5B', 'GPSM1', 'GPT2', 'GPX3', 'GREB1', 'GSN', 'GSTM3', 'GSTM5', 'GSTP1', 'GTF2A1', 'GTPBP10', 'GUCA1B', 'GUCA2A', 'GUCY1A3', 'GULP1', 'GYLTL1B', 'H19', 'HABP2', 'HAP1', 'HBEGF', 'HCK', 'HDHD3', 'HEATR5A', 'HEBP1', 'HEG1', 'HEPH', 'HERPUD1', 'HES1', 'HIC1', 'HIF1A', 'HILPDA', 'HIP1', 'HIRA', 'HIST1H1C', 'HIST1H2BK', 'HIST2H2BE', 'HK1', 'HK2', 'HKDC1', 'HMGB3', 'HMGCS1', 'HMGN5', 'HMOX1', 'HN1', 'HNF1B', 'HNF4A', 'HNMT', 'HOMER2', 'HOPX', 'HOXB2', 'HOXB4', 'HPCAL1', 'HPGD', 'HPN', 'HS3ST1', 'HS3ST3A1', 'HS6ST2', 'HSD11B2', 'HSD17B11', 'HSPA1A', 'HSPA1B', 'HSPA5', 'HSPB6', 'HSPB8', 'HTRA1', 'HUNK', 'HYAL3', 'IBA57', 'ID1', 'ID4', 'IDH1', 'IDH2', 'IER2', 'IER3', 'IFI30', 'IFIT1', 'IFITM2', 'IFNGR1', 'IGFBP6', 'IGFBPL1', 'IGSF3', 'IKBIP', 'IKBKE', 'IKZF3', 'IL11', 'IL15RA', 'IL1RN', 'IL22RA1', 'IL33', 'IMPA2', 'INHBB', 'INPP4B', 'INSIG1', 'INSM1', 'IQGAP2', 'IRAK2', 'IRF1', 'IRS2', 'IRX1', 'IRX2', 'ISG20', 'ISL1', 'ITGA11', 'ITGA1', 'ITGA3', 'ITGA6', 'ITGAV', 'ITGB1', 'ITGB4', 'ITGB8', 'ITIH5', 'ITPR2', 'IVNS1ABP', 'IYD', 'JAM3', 'JARID2', 'JDP2', 'JMJD6', 'JPX', 'JUNB', 'JUN', 'JUP', 'KCNA5', 'KCNE3', 'KCNG1', 'KCNH6', 'KCNJ13', 'KCNJ5', 'KCNJ6', 'KCNJ8', 'KCNK16', 'KCNK5', 'KCNN2', 'KCNN3', 'KCNQ1OT1', 'KCNQ1', 'KCTD12', 'KDELC2', 'KDELR3', 'KIF11', 'KIF12', 'KIF20B', 'KIF21B', 'KIF5C', 'KIT', 'KLB', 'KLF2', 'KLF4', 'KLF5', 'KLF6', 'KLF7', 'KLHL28', 'KLHL31', 'KLHL3', 'KLK10', 'KLK11', 'KREMEN1', 'KRT15', 'KRT17', 'KRTCAP3', 'KYNU', 'L1TD1', 'L2HGDH', 'LAD1', 'LAIR1', 'LAMA1', 'LAMA3', 'LAMB1', 'LAMB2', 'LAMB3', 'LARP6', 'LASP1', 'LBH', 'LCP1', 'LDB2', 'LDLR', 'LEFTY1', 'LFNG', 'LGALS3', 'LGALS9', 'LHFPL2', 'LIFR', 'LIF', 'LIMA1', 'LIMK2', 'LIMS1', 'LIPC', 'LIPH', 'LITAF', 'LMO1', 'LMO2', 'LMO4', 'LMO7', 'LNX2', 'LOXL1', 'LOXL2', 'LPAR1', 'LRP1', 'LRP8', 'LRRC27', 'LRRC2', 'LRRC57', 'LRRC58', 'LRRIQ1', 'LRRK2', 'LRRTM2', 'LSR', 'LSS', 'LTBP4', 'LTB', 'LTF', 'LTV1', 'LURAP1L', 'LXN', 'LY6E', 'LY6H', 'LY96', 'LYN', 'LYPD1', 'LYRM7', 'LZTS1', 'MAB21L3', 'MACC1', 'MAFB', 'MAFF', 'MAL2', 'MALL', 'MAOA', 'MAOB', 'MAP3K9', 'MAPT', 'MARCKSL1', 'MAT1A', 'MCC', 'MCL1', 'MCM2', 'MCM6', 'MCOLN2', 'MDFIC', 'MDFI', 'MDGA1', 'MDK', 'MDM1', 'ME1', 'MEDAG', 'MEF2C', 'MEIS2', 'METRNL', 'METTL21A', 'MEX3A', 'MFAP2', 'MFAP4', 'MFGE8', 'MGAT4B', 'MGLL', 'MGP', 'MICAL2', 'MID1', 'MIR143HG', 'MKNK1', 'MLLT11', 'MLXIPL', 'MMACHC', 'MMP14', 'MNS1', 'MOB3B', 'MOSPD1', 'MOXD1', 'MPPED2', 'MPST', 'MPZL2', 'MRC2', 'MS4A2', 'MSMO1', 'MSRB1', 'MSRB3', 'MSX1', 'MTHFD2', 'MTUS1', 'MVP', 'MYADM', 'MYH9', 'MYL12A', 'MYL12B', 'MYL9', 'MYLK', 'MYO1C', 'MYO5B', 'MYOF', 'MYRF', 'MYZAP', 'N4BP3', 'NAA40', 'NAP1L2', 'NCAM1', 'NCF2', 'NCMAP', 'NCS1', 'NDRG1', 'NDRG2', 'NDUFA4L2', 'NDUFA4', 'NEDD9', 'NEK6', 'NEK8', 'NEURL3', 'NEUROD1', 'NEXN', 'NFATC4', 'NFKBIE', 'NFKBIZ', 'NHSL1', 'NICN1', 'NID1', 'NID2', 'NIPSNAP3B', 'NKD1', 'NLN', 'NLRC3', 'NMB', 'NOL9', 'NOTCH1', 'NOTCH3', 'NOTCH4', 'NPHS1', 'NPR1', 'NPTX2', 'NPY1R', 'NQO1', 'NR0B1', 'NR0B2', 'NR1D1', 'NR2F2', 'NR4A2', 'NR4A3', 'NR5A2', 'NR6A1', 'NRARP', 'NREP', 'NRP2', 'NSG1', 'NT5E', 'NTM', 'NTN4', 'NUAK2', 'NUGGC', 'NUSAP1', 'NYAP2', 'OAF', 'OAS3', 'OCLN', 'ODF2L', 'OGDH', 'OLFM2', 'OLFML1', 'OLFML2B', 'ORAI2', 'ORC4', 'OSGIN1', 'OSMR', 'OVOL1', 'OXR1', 'P2RX1', 'P4HA1', 'P4HA3', 'PACSIN2', 'PAG1', 'PAH', 'PALB2', 'PAMR1', 'PANK1', 'PAQR5', 'PARD6G', 'PARM1', 'PASK', 'PCDH10', 'PCDH17', 'PCDH18', 'PCDH7', 'PCK2', 'PCP4', 'PCSK2', 'PCSK5', 'PDCD4', 'PDDC1', 'PDE1A', 'PDE3B', 'PDE4A', 'PDE4C', 'PDE7B', 'PDE8B', 'PDGFA', 'PDGFB', 'PDGFC', 'PDIA4', 'PDLIM1', 'PDLIM2', 'PDLIM3', 'PDLIM4', 'PDP1', 'PDP2', 'PDX1', 'PEAK1', 'PECAM1', 'PEG10', 'PEMT', 'PGC', 'PGM1', 'PGM2L1', 'PHGDH', 'PHGR1', 'PHLDA1', 'PHLDA2', 'PHLDA3', 'PID1', 'PIEZO1', 'PIGN', 'PIK3IP1', 'PIK3R1', 'PIM1', 'PIM2', 'PIM3', 'PIWIL2', 'PKIB', 'PLA2G15', 'PLA2G4A', 'PLA2G4C', 'PLAT', 'PLBD1', 'PLCD1', 'PLCD3', 'P
#> ℹ [2026-01-27 07:52:30] Use 2000 features to calculate distance
#> Warning: The following features were labelled as variable in 'var.features' but had no corresponding rank in `var.features.rank` and will therefore be ignored: 'A4GALT', 'AADAC', 'AARS2', 'ABCA1', 'ABCC3', 'ABCC4', 'ABCC8', 'ABCC9', 'ABCG2', 'ABHD15', 'ABI3', 'ABL2', 'ABTB2', 'ACACB', 'ACBD7', 'ACE', 'ACHE', 'ACSL3', 'ACSL4', 'ACTG1', 'ACTN1', 'ACTN4', 'ADAM12', 'ADAM9', 'ADAMTS1', 'ADAMTS2', 'ADAMTSL2', 'ADAT1', 'ADCK3', 'ADCY1', 'ADCY3', 'ADCY5', 'ADD3', 'ADM', 'ADRA2A', 'ADRA2C', 'ADRB1', 'ADRBK2', 'AFAP1L2', 'AGR2', 'AGRN', 'AHR', 'AIFM3', 'AIM1L', 'AIM1', 'AJAP1', 'AK5', 'AKAP7', 'ALDH1A1', 'ALDH1A2', 'ALDH2', 'ALDH3A2', 'ALDH3B1', 'ALDH4A1', 'ALOX5AP', 'ALPL', 'AMOTL1', 'AMOTL2', 'ANGPTL1', 'ANO6', 'ANO9', 'ANTXR2', 'AOC2', 'AP1S2', 'AP1S3', 'APOBEC2', 'APOD', 'AQP3', 'AQP4', 'ARHGAP26', 'ARHGAP29', 'ARHGAP6', 'ARHGEF17', 'ARHGEF2', 'ARHGEF3', 'ARHGEF40', 'ARHGEF6', 'ARL14', 'ARL4D', 'ARL6', 'ARMC9', 'ARNTL2', 'ARSJ', 'ARX', 'ASAP1', 'ASCL1', 'ASNS', 'ASPH', 'ASRGL1', 'ASS1', 'ASTN2', 'ASXL3', 'ATCAY', 'ATF3', 'ATF5', 'ATHL1', 'ATP10B', 'ATP11A', 'ATP1A1', 'ATP1B2', 'ATP2A3', 'ATP2B4', 'ATP8B1', 'AURKB', 'B3GNT2', 'B4GALT1', 'B4GALT5', 'BACE2', 'BACH2', 'BAIAP2L1', 'BAIAP3', 'BAMBI', 'BARX2', 'BASP1', 'BATF', 'BAZ1A', 'BBC3', 'BCHE', 'BCL2L15', 'BCL3', 'BCL6B', 'BCL6', 'BDH2', 'BHLHE41', 'BHMT2', 'BIK', 'BIRC5', 'BMF', 'BMP2', 'BMPR2', 'BNC2', 'BRIP1', 'BUB1', 'C1QL1', 'C1QTNF1', 'C1RL', 'C2CD4A', 'C2CD4B', 'CABP4', 'CACNA2D1', 'CADM2', 'CADPS2', 'CALCA', 'CALML4', 'CALU', 'CALY', 'CAMK1D', 'CAMKK1', 'CAMKK2', 'CAPN5', 'CAPN6', 'CARHSP1', 'CARTPT', 'CASP6', 'CAV2', 'CBR1', 'CCDC15', 'CCDC71L', 'CCL28', 'CCND2', 'CCNF', 'CCNG2', 'CD200', 'CD276', 'CD47', 'CD68', 'CD82', 'CDCA3', 'CDH17', 'CDH1', 'CDH23', 'CDH2', 'CDH3', 'CDHR2', 'CDK17', 'CDKN1A', 'CDKN2A', 'CDKN2B', 'CDR2', 'CDT1', 'CDX2', 'CEACAM1', 'CEBPB', 'CELF2', 'CENPF', 'CENPW', 'CERCAM', 'CFI', 'CFLAR', 'CGN', 'CHAC1', 'CHGB', 'CHN2', 'CHRM3', 'CHST1', 'CHSY1', 'CITED2', 'CITED4', 'CLCF1', 'CLCN4', 'CLDN11', 'CLDN19', 'CLDN3', 'CLDN5', 'CLDN6', 'CLDN7', 'CLEC11A', 'CLIC5', 'CLIC6', 'CLMN', 'CLMP', 'CLRN3', 'CLSPN', 'CMPK2', 'CMTM3', 'CMTM7', 'CNIH2', 'CNN2', 'CNN3', 'CNNM1', 'CNTN1', 'COCH', 'COL13A1', 'COL14A1', 'COL16A1', 'COL18A1', 'COL5A3', 'COL9A2', 'COMMD2', 'COMP', 'CORO1C', 'CORO2A', 'COX7A1', 'CPA3', 'CPLX2', 'CPM', 'CRABP2', 'CRADD', 'CREB3L1', 'CREB5', 'CREG2', 'CRIP1', 'CRLF1', 'CRTAC1', 'CRTAP', 'CTHRC1', 'CTNNA2', 'CTSB', 'CTSC', 'CTSS', 'CX3CL1', 'CXADR', 'CXCL12', 'CXCL16', 'CYB5A', 'CYBRD1', 'CYP20A1', 'CYP27B1', 'CYR61', 'CYTH3', 'DAB2IP', 'DACH1', 'DACT1', 'DAG1', 'DBN1', 'DCAF11', 'DCBLD2', 'DCUN1D2', 'DDAH2', 'DDC', 'DDIT3', 'DDX25', 'DDX51', 'DGKA', 'DHCR7', 'DHDH', 'DHODH', 'DHRS2', 'DIXDC1', 'DKK1', 'DMBT1', 'DMC1', 'DNAJB9', 'DNAJC22', 'DNER', 'DOCK4', 'DOCK5', 'DOK5', 'DPEP1', 'DPP9', 'DRAM1', 'DSC2', 'DSG2', 'DTNA', 'DUSP10', 'DUSP14', 'DUSP1', 'DUSP23', 'DUSP2', 'DUSP5', 'DZANK1', 'EBP', 'ECE1', 'ECEL1', 'EDN2', 'EFCAB7', 'EFNB1', 'EFNB3', 'EGFR', 'EGF', 'EGR1', 'EGR4', 'EHD1', 'EHD4', 'EHF', 'EIF4EBP1', 'ELAVL4', 'EMILIN1', 'EMP2', 'ENAH', 'ENG', 'ENPP2', 'EPAS1', 'EPDR1', 'EPHA2', 'EPHB2', 'EPHX1', 'EPS8L1', 'ERBB2', 'ERBB3', 'ERO1LB', 'ERO1L', 'ERRFI1', 'ESRRG', 'ETS2', 'ETV1', 'EVA1B', 'EVC2', 'EXT1', 'F10', 'F11R', 'F2RL1', 'F5', 'FA2H', 'FABP5', 'FADS1', 'FADS2', 'FAM101B', 'FAM105A', 'FAM107B', 'FAM129B', 'FAM134B', 'FAM155A', 'FAM159B', 'FAM161A', 'FAM162A', 'FAM163A', 'FAM20C', 'FAM217B', 'FAM227A', 'FAM43A', 'FAM46B', 'FAM46C', 'FAM73A', 'FAM84A', 'FAM84B', 'FBLIM1', 'FBLN1', 'FBLN5', 'FBP1', 'FBXL18', 'FBXO2', 'FBXO6', 'FCER1G', 'FDFT1', 'FERMT2', 'FEV', 'FEZ1', 'FFAR2', 'FFAR4', 'FGD2', 'FGD4', 'FGF7', 'FGFBP1', 'FGFR2', 'FGFR3', 'FGL2', 'FHL2', 'FKBP10', 'FKBP11', 'FKBP5', 'FLNA', 'FNDC4', 'FOLR1', 'FOSB', 'FOSL2', 'FOXC1', 'FOXM1', 'FOXQ1', 'FRAS1', 'FRMD4B', 'FSCN1', 'FXN', 'FXYD3', 'FXYD5', 'FXYD6', 'FZD5', 'G0S2', 'GAD2', 'GADD45A', 'GADD45B', 'GADD45G', 'GALE', 'GALM', 'GALNT2', 'GALNT3', 'GAL', 'GAS6', 'GAS7', 'GATA2', 'GCK', 'GCLC', 'GCNT1', 'GC', 'GDPD1', 'GFOD2', 'GFRA1', 'GGT1', 'GGT5', 'GHR', 'GINS3', 'GINS4', 'GJA1', 'GJA4', 'GJB1', 'GJB3', 'GJC1', 'GK5', 'GK', 'GLDC', 'GLI2', 'GLIPR2', 'GLT1D1', 'GLUL', 'GMDS', 'GMEB1', 'GMFG', 'GMNN', 'GNAL', 'GNPNAT1', 'GNPTAB', 'GOLM1', 'GOT1', 'GPC1', 'GPC6', 'GPR155', 'GPR160', 'GPR161', 'GPR4', 'GPRC5A', 'GPRC5B', 'GPSM1', 'GPT2', 'GPX3', 'GREB1', 'GSN', 'GSTM3', 'GSTM5', 'GSTP1', 'GTF2A1', 'GTPBP10', 'GUCA1B', 'GUCA2A', 'GUCY1A3', 'GULP1', 'GYLTL1B', 'H19', 'HABP2', 'HAP1', 'HBEGF', 'HCK', 'HDHD3', 'HEATR5A', 'HEBP1', 'HEG1', 'HEPH', 'HERPUD1', 'HES1', 'HIC1', 'HIF1A', 'HILPDA', 'HIP1', 'HIRA', 'HIST1H1C', 'HIST1H2BK', 'HIST2H2BE', 'HK1', 'HK2', 'HKDC1', 'HMGB3', 'HMGCS1', 'HMGN5', 'HMOX1', 'HN1', 'HNF1B', 'HNF4A', 'HNMT', 'HOMER2', 'HOPX', 'HOXB2', 'HOXB4', 'HPCAL1', 'HPGD', 'HPN', 'HS3ST1', 'HS3ST3A1', 'HS6ST2', 'HSD11B2', 'HSD17B11', 'HSPA1A', 'HSPA1B', 'HSPA5', 'HSPB6', 'HSPB8', 'HTRA1', 'HUNK', 'HYAL3', 'IBA57', 'ID1', 'ID4', 'IDH1', 'IDH2', 'IER2', 'IER3', 'IFI30', 'IFIT1', 'IFITM2', 'IFNGR1', 'IGFBP6', 'IGFBPL1', 'IGSF3', 'IKBIP', 'IKBKE', 'IKZF3', 'IL11', 'IL15RA', 'IL1RN', 'IL22RA1', 'IL33', 'IMPA2', 'INHBB', 'INPP4B', 'INSIG1', 'INSM1', 'IQGAP2', 'IRAK2', 'IRF1', 'IRS2', 'IRX1', 'IRX2', 'ISG20', 'ISL1', 'ITGA11', 'ITGA1', 'ITGA3', 'ITGA6', 'ITGAV', 'ITGB1', 'ITGB4', 'ITGB8', 'ITIH5', 'ITPR2', 'IVNS1ABP', 'IYD', 'JAM3', 'JARID2', 'JDP2', 'JMJD6', 'JPX', 'JUNB', 'JUN', 'JUP', 'KCNA5', 'KCNE3', 'KCNG1', 'KCNH6', 'KCNJ13', 'KCNJ5', 'KCNJ6', 'KCNJ8', 'KCNK16', 'KCNK5', 'KCNN2', 'KCNN3', 'KCNQ1OT1', 'KCNQ1', 'KCTD12', 'KDELC2', 'KDELR3', 'KIF11', 'KIF12', 'KIF20B', 'KIF21B', 'KIF5C', 'KIT', 'KLB', 'KLF2', 'KLF4', 'KLF5', 'KLF6', 'KLF7', 'KLHL28', 'KLHL31', 'KLHL3', 'KLK10', 'KLK11', 'KREMEN1', 'KRT15', 'KRT17', 'KRTCAP3', 'KYNU', 'L1TD1', 'L2HGDH', 'LAD1', 'LAIR1', 'LAMA1', 'LAMA3', 'LAMB1', 'LAMB2', 'LAMB3', 'LARP6', 'LASP1', 'LBH', 'LCP1', 'LDB2', 'LDLR', 'LEFTY1', 'LFNG', 'LGALS3', 'LGALS9', 'LHFPL2', 'LIFR', 'LIF', 'LIMA1', 'LIMK2', 'LIMS1', 'LIPC', 'LIPH', 'LITAF', 'LMO1', 'LMO2', 'LMO4', 'LMO7', 'LNX2', 'LOXL1', 'LOXL2', 'LPAR1', 'LRP1', 'LRP8', 'LRRC27', 'LRRC2', 'LRRC57', 'LRRC58', 'LRRIQ1', 'LRRK2', 'LRRTM2', 'LSR', 'LSS', 'LTBP4', 'LTB', 'LTF', 'LTV1', 'LURAP1L', 'LXN', 'LY6E', 'LY6H', 'LY96', 'LYN', 'LYPD1', 'LYRM7', 'LZTS1', 'MAB21L3', 'MACC1', 'MAFB', 'MAFF', 'MAL2', 'MALL', 'MAOA', 'MAOB', 'MAP3K9', 'MAPT', 'MARCKSL1', 'MAT1A', 'MCC', 'MCL1', 'MCM2', 'MCM6', 'MCOLN2', 'MDFIC', 'MDFI', 'MDGA1', 'MDK', 'MDM1', 'ME1', 'MEDAG', 'MEF2C', 'MEIS2', 'METRNL', 'METTL21A', 'MEX3A', 'MFAP2', 'MFAP4', 'MFGE8', 'MGAT4B', 'MGLL', 'MGP', 'MICAL2', 'MID1', 'MIR143HG', 'MKNK1', 'MLLT11', 'MLXIPL', 'MMACHC', 'MMP14', 'MNS1', 'MOB3B', 'MOSPD1', 'MOXD1', 'MPPED2', 'MPST', 'MPZL2', 'MRC2', 'MS4A2', 'MSMO1', 'MSRB1', 'MSRB3', 'MSX1', 'MTHFD2', 'MTUS1', 'MVP', 'MYADM', 'MYH9', 'MYL12A', 'MYL12B', 'MYL9', 'MYLK', 'MYO1C', 'MYO5B', 'MYOF', 'MYRF', 'MYZAP', 'N4BP3', 'NAA40', 'NAP1L2', 'NCAM1', 'NCF2', 'NCMAP', 'NCS1', 'NDRG1', 'NDRG2', 'NDUFA4L2', 'NDUFA4', 'NEDD9', 'NEK6', 'NEK8', 'NEURL3', 'NEUROD1', 'NEXN', 'NFATC4', 'NFKBIE', 'NFKBIZ', 'NHSL1', 'NICN1', 'NID1', 'NID2', 'NIPSNAP3B', 'NKD1', 'NLN', 'NLRC3', 'NMB', 'NOL9', 'NOTCH1', 'NOTCH3', 'NOTCH4', 'NPHS1', 'NPR1', 'NPTX2', 'NPY1R', 'NQO1', 'NR0B1', 'NR0B2', 'NR1D1', 'NR2F2', 'NR4A2', 'NR4A3', 'NR5A2', 'NR6A1', 'NRARP', 'NREP', 'NRP2', 'NSG1', 'NT5E', 'NTM', 'NTN4', 'NUAK2', 'NUGGC', 'NUSAP1', 'NYAP2', 'OAF', 'OAS3', 'OCLN', 'ODF2L', 'OGDH', 'OLFM2', 'OLFML1', 'OLFML2B', 'ORAI2', 'ORC4', 'OSGIN1', 'OSMR', 'OVOL1', 'OXR1', 'P2RX1', 'P4HA1', 'P4HA3', 'PACSIN2', 'PAG1', 'PAH', 'PALB2', 'PAMR1', 'PANK1', 'PAQR5', 'PARD6G', 'PARM1', 'PASK', 'PCDH10', 'PCDH17', 'PCDH18', 'PCDH7', 'PCK2', 'PCP4', 'PCSK2', 'PCSK5', 'PDCD4', 'PDDC1', 'PDE1A', 'PDE3B', 'PDE4A', 'PDE4C', 'PDE7B', 'PDE8B', 'PDGFA', 'PDGFB', 'PDGFC', 'PDIA4', 'PDLIM1', 'PDLIM2', 'PDLIM3', 'PDLIM4', 'PDP1', 'PDP2', 'PDX1', 'PEAK1', 'PECAM1', 'PEG10', 'PEMT', 'PGC', 'PGM1', 'PGM2L1', 'PHGDH', 'PHGR1', 'PHLDA1', 'PHLDA2', 'PHLDA3', 'PID1', 'PIEZO1', 'PIGN', 'PIK3IP1', 'PIK3R1', 'PIM1', 'PIM2', 'PIM3', 'PIWIL2', 'PKIB', 'PLA2G15', 'PLA2G4A', 'PLA2G4C', 'PLAT', 'PLBD1', 'PLCD1', 'PLCD3', 'P
#> ℹ [2026-01-27 07:52:30] Use raw method to find neighbors
#> ℹ [2026-01-27 07:52:30] Running UMAP projection
ProjectionPlot(
  srt_query = srt_query,
  srt_ref = srt_ref,
  query_group = "celltype",
  ref_group = "celltype"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: Removed 6 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 6 rows containing missing values or values outside the scale range
#> (`geom_point()`).