Loading Libraries
library(rPanglaoDB)
library(Seurat)
library(harmony)
library(Nebulosa)
library(ggplot2)
library(ggrepel)
library(fgsea)
library(GSVA)
library(statsExpressions)
BIOP <- gmtPathways('https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=BioPlanet_2019')
LEC <- getMarkers(include = c('PECAM1', 'PDPN', 'PROX1'))
LEC <- getSamples(srs = unique(LEC$SRS),
specie = 'Homo sapiens',
celltype = 'Endothelial cells',
include = c('PECAM1', 'PDPN', 'PROX1'))
| | 0 % ~calculating
|+++++++++++++++++ | 33% ~02m 55s
|++++++++++++++++++++++++++++++++++ | 67% ~01m 04s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 41s
BEC <- getMarkers(include = c('PECAM1', 'VWF'), exclude = c('PDPN', 'ACTA2'))
BEC <- getSamples(srs = unique(BEC$SRS),
specie = 'Homo sapiens',
celltype = 'Endothelial cells',
include = c('PECAM1', 'VWF'),
exclude = c('PDPN', 'ACTA2'))
| | 0 % ~calculating
|++ | 3 % ~26m 44s
|+++ | 6 % ~28m 27s
|+++++ | 8 % ~34m 09s
|++++++ | 11% ~33m 32s
|+++++++ | 14% ~27m 17s
|+++++++++ | 17% ~24m 30s
|++++++++++ | 19% ~21m 32s
|++++++++++++ | 22% ~19m 35s
|+++++++++++++ | 25% ~17m 40s
|++++++++++++++ | 28% ~16m 43s
|++++++++++++++++ | 31% ~15m 51s
|+++++++++++++++++ | 33% ~15m 07s
|+++++++++++++++++++ | 36% ~14m 16s
|++++++++++++++++++++ | 39% ~13m 40s
|+++++++++++++++++++++ | 42% ~12m 57s
|+++++++++++++++++++++++ | 44% ~12m 35s
|++++++++++++++++++++++++ | 47% ~11m 58s
|+++++++++++++++++++++++++ | 50% ~11m 31s
|+++++++++++++++++++++++++++ | 53% ~10m 52s
|++++++++++++++++++++++++++++ | 56% ~10m 22s
|++++++++++++++++++++++++++++++ | 58% ~09m 43s
|+++++++++++++++++++++++++++++++ | 61% ~09m 26s
|++++++++++++++++++++++++++++++++ | 64% ~09m 21s
|++++++++++++++++++++++++++++++++++ | 67% ~09m 08s
|+++++++++++++++++++++++++++++++++++ | 69% ~09m 06s
|+++++++++++++++++++++++++++++++++++++ | 72% ~08m 44s
|++++++++++++++++++++++++++++++++++++++ | 75% ~07m 49s
|+++++++++++++++++++++++++++++++++++++++ | 78% ~06m 49s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~05m 54s
|++++++++++++++++++++++++++++++++++++++++++ | 83% ~05m 00s
|++++++++++++++++++++++++++++++++++++++++++++ | 86% ~04m 08s
|+++++++++++++++++++++++++++++++++++++++++++++ | 89% ~03m 17s
|++++++++++++++++++++++++++++++++++++++++++++++ | 92% ~02m 28s
|++++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~01m 38s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~50s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=29m 28s
Endothelial <- merge(LEC, BEC)
Endothelial <- RunHarmony(Endothelial, group.by.vars = 'orig.ident')
Harmony 1/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 2/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 3/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 4/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 5/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**********************

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