A. viSNE SPADE X-shift Citrus Phenograph B.

% of events
ViSNE/Boolean SPADE
CD45

CD4+
CD8+
CD19+
CD11b+ CD64+
CD11b+ CD64-
X-shift Phenograph CD45+
CD19

CD45-
NKp46+

C. # of clusters/nodes in phenotype
CD4

X-shift Phenograph SPADE

CD4+
CD8+
CD19+
CD11b+ CD64+
CD11b+ CD64-
CD45+
CD45-
NKp46+
CD8

Total=45 Total=29 Total=45

D. 6
Citrus, daughter #82243
SPADE, node #1
X-shift, cluster #515
Phenograph, cluster #8

Median Expression
CD11c

2
NKp46

Tbet
Tim3
Lag3
IkBa
CD19
NKp46
Ki67
PDL2
CD64
PDL1
IRF4
Sig F
FoxP3
KLRG1
Bcatenin
CD127
CD11c
GITR
MHCI
CD69
CD8
CD11b
CD25
Gr-1
p4eBP1
CD3
CTLA4
PD1
Sca1
CD45
CD44
CD4
CD117
MHCII
ICOS
E. 117
MHC
II ICOS Tbet Tim3
Lag
3
IkB
CD a
4 CD
CD 19
4
4
CD

NK
CD64

p4
45

6
CD

Ki6
7 P
1
Sca

DL2
PD1

CD64 PDL1 IRF4 SigF

Citrus, daughter #82243
CTLA4

SPADE, node #1
X-shift, cluster #515
CD11b

Phenograph, cluster #8
CD3
BP1

F
p4e

oxP
3
-1

KL
Gr

viSNE X-shift Phenograph

G1 R

F.
5
D2

Bc
C at
en
b in
D11 CD
C 127
CD8
2,000

CD1
CD69 MHCI GITR 1c

G.
tSNE2

19 clusters tSNE1 20 clusters 50

# of input events per sample

# of Defined Clusters

40 X-shift
5,000

30
tSNE2

23 clusters tSNE1 28 clusters

20
PhenoGraph

10
9,141 #1

0
tSNE2

00

00

#1

#2

00

tSNE1
32 clusters 29 clusters
0

,0
1

1
2,

5,

14

14

20
9,

9,

# of input events per sample

9,141 #2

H.
tSNE2

% of events
32 clusters tSNE1
tSNE130 clusters 0 5 10 15 20 # of
Range clusters <1%
# of input events per sample

2,000 (0.42-15.8) 3 of 20
20,000

Incompatible
5,000 (0.48-15.7) 5 of 28
setting for
algorithm
tSNE2

tSNE1
9,141 #1 (0.14-11.8) 7 of 29
46 clusters 37 clusters
9,141 #2 (0.02-9.83) 9 of 30
(1,263,690)
All events

Insufficient Insufficient 20,000 (0.02-7.96) 14 of 37

processing processing
power power 1%
Figure 7
Kimball et al