2 dimensional quadrant plot

Question

[bobbybleek]

Hey everyone,

I am working with single cell RNA seq data and I am trying to create one of the plots but I am unable to. I am fairly new to this, I am using R studio to make this plot.

nihms-1532254-f0004.jpeg

I have a seurat object which looks like this

orig.ident
nCount_RNA
nFeature_RNA
percent.mt
RNA_snn_res.0.4
seurat_clusters
pANN_0.25_0.09_609
DF.classifications_0.25_0.09_609
customclassif
RNA_snn_res.0.1
clustername
PMT1
S.Score
G2M.Score
Phase
nCount_SCT
nFeature_SCT
SCT_snn_res.0.1
MES1
NPC1
AC1
SCT_snn_res.0.3
SCT_snn_res.0.5
SCT_snn_res.0.7
SCT_snn_res.1
wtsal_AAACCCAAGGTAATCA-1
wtsal
3268
1698
1.83598531
5
6
0.20361248
Singlet
Endothelial cells
1
cluster1
5.761777e-01
-7.746181e-02
-0.1260512510
G1
2366
1654
1
-0.2310490602
-0.203696678
-0.144518588
0
2
6
6
wtsal_AAACCCACATATCTGG-1
wtsal
690
489
0.72463768
3
4
0.08757526
Singlet
Schwann precursor cells
0
cluster0
-2.726967e-01
-5.061890e-02
0.0150902896
G2M
1347
478
0
-0.1552159182
0.239995713
-0.083305113
1
1
1
4
wtsal_AAACGAAAGCAACTTC-1
wtsal
3277
1584
0.54928288
3
3
0.10454297
Singlet
Schwann precursor cells
0
cluster0
-2.840240e-01
-4.201707e-02
0.0061154489
G2M
2346
1562
0
-0.2142643154
0.109861229
0.301320875
1
4
5
3
wtsal_AAACGAAAGGAGTCTG-1
wtsal
1300
853
0.23076923
7
11
0.26819923
Singlet
Oligodendrocyte precursor cells
2
cluster2
-3.459902e-01
-2.229163e-03
-0.0800638282
G1
1481
837
2
-0.0814124810
-0.034657359
0.034657359
2
0
12
11
wtsal_AAACGAAGTCGTGTTA-1
wtsal
529
412
0.94517958
3
4
0.09906951
Singlet
Schwann precursor cells
0
cluster0
2.264688e-01
-3.106937e-02
0.0561632523
G2M
1192
422
0
0.2583561234
-0.096780025
-0.069314718
1
1
1
4
wtsal_AAACGAAGTCTAGTGT-1
wtsal
5167
1827
3.44493904
5
12
0.24356869
Singlet
Endothelial cells
1
cluster1
-3.448173e-01
-5.277532e-02
-0.1324324128
G1
1988
960
1
-0.2754747194
-0.169104339
-0.335649545
0
8
11
12
wtsal_AAACGCTAGGAGATAG-1
wtsal
800
566
1.12500000
3
5
0.09031199
Singlet
Schwann precursor cells
0
cluster0
1.041076e-01
-3.610486e-02
-0.0307871112
G1
1488
559
0
-0.1188246118
-0.082395922
0.120391565
1
1
3
5
wtsal_AAACGCTAGTAGGATT-1
wtsal
1729
1019
1.33024870
7
11
0.26655720
Singlet
Oligodendrocyte precursor cells
2
cluster2
6.528951e-01
-8.214611e-02
-0.1042812039
G1
1720
997
2
0.0825021329
0.248490665
-0.047738563
2
0
12
11
wtsal_AAACGCTCAGAGCCCT-1
wtsal
698
515
0.57306590
12
7
0.10673235
Singlet
Endothelial cells
3
cluster3
-5.459186e-01
-4.524667e-02
-0.0807996971
G1
1368
511
1
-0.0498983706
-0.054930614
-0.027465307
0
2
7
7
wtsal_AAAGGATAGCGCCTAC-1
wtsal
4050
1711
4.44444444
12
9
0.23535851
Singlet
Endothelial cells
3
cluster3
6.704685e-01
-1.242019e-02
-0.0882920588
G1
2318
1422
0
0.4862858269
-0.235147679
0.060791553
4
7
9
9
wtsal_AAAGGATAGGATACAT-1
wtsal
1739
1038
0.17251294
7
11
0.19923372
Singlet
Oligodendrocyte precursor cells
2
cluster2
5.315519e-01
-4.341325e-03
-0.0675722487
G1
1732
1023
2
0.1310532897
0.325634690
-0.148766064
2
0
12
11
wtsal_AAAGGATCATGACCCG-1
wtsal
504
402
2.57936508
3
4
0.09195402
Singlet
Schwann precursor cells
0
cluster0
-1.214774e-01
2.123880e-02
0.2968659011
G2M
1130
418
0
-0.1446724076
0.033354459
0.155958116
1
1
1
4
wtsal_AAAGGTAAGACAGCGT-1
wtsal
598
433
3.17725753
7
4
0.09140668
Singlet
Oligodendrocyte precursor cells
0
cluster0
-1.149932e-01
1.816482e-02
-0.0694119278
S
1283
434
0
-0.1915660342
0.274653072
0.089981682
1
1
1
4
wtsal_AAAGGTATCGGCTCTT-1
wtsal
3887
1996
1.33779264
5
6
0.27805145
Singlet
Endothelial cells
1
cluster1
2.169525e-02
-3.447223e-02
-0.0489689474
G1
2420
1730
1
0.4738285049
0.086953961
0.030409883
0
2
6
6
wtsal_AAAGTCCAGCTGCGAA-1
wtsal
696
431
1.72413793
7
0
0.14668856
Singlet
Oligodendrocyte precursor cells
2
cluster2
-2.607525e-01
-3.912846e-02
0.0517844251
G2M
1389
427
2
-0.3080904917
-0.054930614
-0.117053281
2
0
1
0
wtsal_AAAGTCCCACAACGTT-1
wtsal
580
436
1.03448276
7
0
0.10618500
Singlet
Oligodendrocyte precursor cells
2
cluster2
-2.322954e-01
-5.493115e-02
-0.0780277785
G1
1265
440
2
-0.2228719724
0.223969934
0.238354037
2
0
1
0

[bobbybleek]

I don't know why my picture is npot visible but this is the image of the plot of fig3F https://europepmc.org/articles/PMC6703186/figure/F3/

[GenoMax]

In edit window use the button after 101010 button to select and attach the image you want to upload to biostars.

[Ram]

You need to copy-paste the Seurat object better, right now it's just a long unstructured list.

[GenoMax]

On trying to format it with 101010 code button it was converted to that list. If it looks wrong then OP can fix.

[jared.andrews07]

Have you scored the genesets using the AddScoreModule function?

Once you do that, you can calculate the coordinates of each cell based on the method described in the paper.