Application Case 2: Endothelial cells

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%
[----|----|----|----|----|----|----|----|----|----|
**********************