scGSVA: GSVA for single cell RNA seq analysis.
scGSVA provides wrap functions to do GSVA analysis for single cell data. And scGSVA includes functions to build annotation for almost all species. scGSVA also provides function to generate figures based on the GSVA results. scGSVA provides functions to generate annotation data which can be used in the analysis.
Installation
library(devtools)
install_github("guokai8/scGSVA")Examples
set.seed(123)
library(scGSVA) ## Attaching SeuratObjectdata(pbmcs)
hsko<-buildAnnot(species="human",keytype="SYMBOL",anntype="KEGG")## 'select()' returned 1:many mapping between keys and columnsres<-scgsva(pbmcs,hsko)## Setting parallel calculations through a MulticoreParam back-end
## with workers=4 and tasks=100.
## Estimating ssGSEA scores for 117 gene sets.
##
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|======================================================================| 100%vlnPlot(res,features="Wnt.signaling.pathway",group_by="groups")
dotPlot(res,features="Wnt.signaling.pathway",group_by="groups")
ridgePlot(res,features="Wnt.signaling.pathway",group_by="groups")## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## Picking joint bandwidth of 0.0451
featurePlot(res,features="Wnt.signaling.pathway", reduction="tsne", group_by="groups")
Heatmap(res,group_by="groups")
## find significant pathways across groups
head(findPathway(res,group = "groups"))## logFC AveExpr t
## Endocytosis -0.05092853 -0.026558556 -2.131606
## Natural.killer.cell.mediated.cytotoxicity 0.07192093 -0.013542222 2.018542
## Butanoate.metabolism -0.04436583 0.092388778 -1.876971
## SNARE.interactions.in.vesicular.transport -0.04760937 0.212333077 -1.819595
## Acute.myeloid.leukemia -0.06306390 0.009388878 -1.799302
## Adherens.junction -0.06306390 0.009388878 -1.799302
## P.Value adj.P.Val B
## Endocytosis 0.03599950 0.6580067 -3.757155
## Natural.killer.cell.mediated.cytotoxicity 0.04676743 0.6580067 -3.960868
## Butanoate.metabolism 0.06403943 0.6580067 -4.201838
## SNARE.interactions.in.vesicular.transport 0.07243017 0.6580067 -4.294961
## Acute.myeloid.leukemia 0.07560918 0.6580067 -4.327263
## Adherens.junction 0.07560918 0.6580067 -4.327263
## comparision
## Endocytosis g1_vs_g2
## Natural.killer.cell.mediated.cytotoxicity g1_vs_g2
## Butanoate.metabolism g1_vs_g2
## SNARE.interactions.in.vesicular.transport g1_vs_g2
## Acute.myeloid.leukemia g1_vs_g2
## Adherens.junction g1_vs_g2head(sigPathway(res, group = "groups"))## Registered S3 method overwritten by 'cli':
## method from
## print.boxx spatstat.geom## # A tibble: 6 x 6
## Path group1 group2 statistic p p.adj
## <chr> <chr> <chr> <dbl> <dbl> <dbl>
## 1 Acute.myeloid.leukemia g1 g2 596 0.0586 0.545
## 2 Adherens.junction g1 g2 596 0.0586 0.545
## 3 Adipocytokine.signaling.pathway g1 g2 882. 0.384 0.712
## 4 African.trypanosomiasis g1 g2 678. 0.274 0.712
## 5 Allograft.rejection g1 g2 958 0.11 0.585
## 6 Alzheimer.disease g1 g2 909 0.261 0.712## extract specific pathways with expression value
head(genes(res, features = "Wnt.signaling.pathway"))## GeneID PATH Annot ATGCCAGAACGACT CATGGCCTGTGCAT
## 10253 PPP3CC 04310 Wnt signaling pathway 0 0
## 12724 TCF7 04310 Wnt signaling pathway 0 0
## GAACCTGATGAACC TGACTGGATTCTCA AGTCAGACTGCACA TCTGATACACGTGT
## 10253 0 0 0 1
## 12724 1 0 1 0
## TGGTATCTAAACAG GCAGCTCTGTTTCT GATATAACACGCAT AATGTTGACAGTCA
## 10253 0 0 0 0
## 12724 0 0 1 0
## AGGTCATGAGTGTC AGAGATGATCTCGC GGGTAACTCTAGTG CATGAGACACGGGA
## 10253 0 1 0 1
## 12724 0 1 0 0
## TACGCCACTCCGAA CTAAACCTGTGCAT GTAAGCACTCATTC TTGGTACTGAATCC
## 10253 0 3 0 0
## 12724 0 0 0 0
## CATCATACGGAGCA TACATCACGCTAAC TTACCATGAATCGC ATAGGAGAAACAGA
## 10253 1 0 0 0
## 12724 0 0 0 0
## GCGCACGACTTTAC ACTCGCACGAAAGT ATTACCTGCCTTAT CCCAACTGCAATCG
## 10253 0 0 0 0
## 12724 0 0 0 0
## AAATTCGAATCACG CCATCCGATTCGCC TCCACTCTGAGCTT CATCAGGATGCACA
## 10253 0 0 0 0
## 12724 0 0 0 0
## CTAAACCTCTGACA GATAGAGAAGGGTG CTAACGGAACCGAT AGATATACCCGTAA
## 10253 0 0 0 0
## 12724 0 0 0 0
## TACTCTGAATCGAC GCGCATCTTGCTCC GTTGACGATATCGG ACAGGTACTGGTGT
## 10253 0 1 0 0
## 12724 0 0 0 0
## GGCATATGCTTATC CATTACACCAACTG TAGGGACTGAACTC GCTCCATGAGAAGT
## 10253 1 0 0 0
## 12724 0 1 0 0
## TACAATGATGCTAG CTTCATGACCGAAT CTGCCAACAGGAGC TTGCATTGAGCTAC
## 10253 0 0 0 0
## 12724 1 1 2 0
## AAGCAAGAGCTTAG CGGCACGAACTCAG GGTGGAGATTACTC GGCCGATGTACTCT
## 10253 0 1 0 0
## 12724 0 0 0 1
## CGTAGCCTGTATGC TGAGCTGAATGCTG CCTATAACGAGACG ATAAGTTGGTACGT
## 10253 0 0 0 0
## 12724 0 0 0 0
## AAGCGACTTTGACG ACCAGTGAATACCG ATTGCACTTGCTTT CTAGGTGATGGTTG
## 10253 0 0 0 0
## 12724 0 0 0 0
## GCACTAGACCTTTA CATGCGCTAGTCAC TTGAGGACTACGCA ATACCACTCTAAGC
## 10253 0 0 0 0
## 12724 0 1 1 0
## CATATAGACTAAGC TTTAGCTGTACTCT GACATTCTCCACCT ACGTGATGCCATGA
## 10253 0 0 0 0
## 12724 0 0 0 0
## ATTGTAGATTCCCG GATAGAGATCACGA AATGCGTGGACGGA GCGTAAACACGGTT
## 10253 0 0 0 0
## 12724 1 0 0 0
## ATTCAGCTCATTGG GGCATATGGGGAGT ATCATCTGACACCA GTCATACTTCGCCT
## 10253 0 0 0 0
## 12724 0 0 0 0
## TTACGTACGTTCAG GAGTTGTGGTAGCT GACGCTCTCTCTCG AGTCTTACTTCGGA
## 10253 0 0 0 0
## 12724 0 0 0 0
## GGAACACTTCAGAC CTTGATTGATCTTC
## 10253 0 0
## 12724 0 0