R/enrich_gradient.R
enrich_gradient.Rdenrich_gradient() calculates over-representation statistics
(ORA) using a ranking of genes from distance_based_analysis()
For ORA using an external or already defined interest list of genes and
gene sets, use leapR functions directly
enrich_gradient(
spe,
assay_name,
geneset,
feature_column,
ranking_column,
method = "ztest"
)SpatialExperiment object containing spatial omics data and spatial diffex results
name of assay
in GMT format
Column of rowData that maps to gene set
Column of rowData that maps to ranks
Rank enrichmemnt method used by leapR. Default is ztest
A dataframe containing results from over-representation analysis of members of gene sets in the interest list of genes based on filtering criteria above.
data(smallPancData)
data(pancMeta)
data(protMeta)
img0.spe <- convert_to_spe(smallPancData$Image_0,
pancMeta,
protMeta,
feature_meta_colname = "pancProts",
image_files = system.file("extdata", "Image_0.png", package = "spammR"),
image_sample_ids = "Image0",
spatial_coords_colnames = c("x_pixels", "y_pixels"),
sample_id = "Image0",
image_ids = "Image0"
)
#> Note: Only mapping metadata for 2986 features out of 3000 data points
img0.spe <- distance_based_analysis(img0.spe,
"proteomics",
sampleCategoryCol = "IsletOrNot",
sampleCategoryValue = "Islet"
)
library(leapR)
data("krbpaths")
rank.res <- enrich_gradient(img0.spe,
geneset = krbpaths,
feature_column = "PrimaryGeneName",
ranking_column = "IsletDistancespearmanCor"
)
head(rank.res)
#> ingroup_n
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL 16
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE 8
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS 15
#> REACTOME_STEROID_METABOLISM 18
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS 18
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK 9
#> ingroupnames
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL C3, IGKC, HLA-B, HLA-A, ITGB2, ICAM1, ITGB1, HLA-C, CDH1, IFITM1, HLA-E, HLA-G, CD34, CD81, B2M, CXADR
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE POLR1C, POLR1A, POLR1D, UBTF, MAPK3, CCNH, MNAT1, POLR2H
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS GNG7, AGT, C3, C5, NPY, ANXA1, GNAI2, GNAI3, CXCL12, GNG2, SST, GNB1, GNB2, GNAI1, GNG5
#> REACTOME_STEROID_METABOLISM SLC27A2, ABCC3, CYP7B1, TM7SF2, ALB, SCP2, FDFT1, LSS, FABP6, HSD17B4, MVD, HSD17B7, MVK, LBR, EBP, PMVK, NSDHL, CYP51A1
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS GNG7, UTS2, AGT, GCG, ANXA1, CHRM3, DGKA, PIK3R1, GNA11, GNAQ, GNG2, GNB1, GNB2, GNG5, PLCB3, DGKZ, ITPR2, ITPR1
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK MCF2L, MAPK8, VAV2, RAC1, AKAP13, ABR, ARHGEF7, ARHGEF16, ARHGEF18
#> ingroup_mean
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL 0.6957938
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE -0.7181860
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS 0.4795099
#> REACTOME_STEROID_METABOLISM 0.7851146
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS 0.4246414
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK -0.7748090
#> outgroup_n
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL 2986
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE 2986
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS 2986
#> REACTOME_STEROID_METABOLISM 2986
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS 2986
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK 2986
#> outgroup_mean
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL -0.003748384
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE 0.001929311
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS -0.002420952
#> REACTOME_STEROID_METABOLISM -0.004761477
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS -0.002575319
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK 0.002342385
#> zscore
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL 0.9340115
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE -0.5846516
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS 0.5242025
#> REACTOME_STEROID_METABOLISM 0.8686835
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS 0.4936846
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK -0.7970220
#> oddsratio
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL 7.163636
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE -6.503451
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS 6.379465
#> REACTOME_STEROID_METABOLISM 6.181998
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS 5.320742
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK -5.311823
#> pvalue
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL 7.856505e-13
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE 7.849792e-11
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS 1.777083e-10
#> REACTOME_STEROID_METABOLISM 6.329517e-10
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS 1.033449e-07
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK 1.085339e-07
#> BH_pvalue
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL 4.886746e-10
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE 2.441285e-08
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS 3.684485e-08
#> REACTOME_STEROID_METABOLISM 9.842398e-08
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS 1.125135e-05
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK 1.125135e-05
#> SignedBH_pvalue
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL 4.886746e-10
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE -2.441285e-08
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS 3.684485e-08
#> REACTOME_STEROID_METABOLISM 9.842398e-08
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS 1.125135e-05
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK -1.125135e-05
#> background_n
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL NA
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE NA
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS NA
#> REACTOME_STEROID_METABOLISM NA
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS NA
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK NA
#> background_mean
#> REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL NA
#> REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE NA
#> REACTOME_G_ALPHA_I_SIGNALLING_EVENTS NA
#> REACTOME_STEROID_METABOLISM NA
#> REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS NA
#> REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK NA