Last updated: 2019-05-15

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html 5fe9f95 Pytrik Folkertsma 2019-05-14 Build site.
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Rmd 0271051 Pytrik Folkertsma 2019-05-07 Updated notebook ECM metabolic genes
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html 2013572 Pytrik Folkertsma 2019-04-12 Build site.
Rmd 2b8079f Pytrik Folkertsma 2019-04-12 Metabolic and ECM genes 
library(Seurat)
library(knitr)
library(kableExtra)
library(dplyr)
seurobj <- readRDS('output/seurat_objects/180831/10x-180831')
markers <- read.table('output/markergenes/180831/markers_10x-180831_upperbranch_lowerbranch_negbinom.tsv', header=T)

Metabolic genes

markers_metabolic <- markers[markers$avg_logFC > 0,]
markers_metabolic <- markers_metabolic[order(-markers_metabolic$avg_logFC),]
kable(markers_metabolic) %>%
  kable_styling(bootstrap_options = "striped", full_width = F)
p_val avg_logFC pct.1 pct.2 p_val_adj gene
1 0 2.3668674 0.814 0.452 0 SCD
2 0 1.9345684 0.944 0.558 0 FABP5
3 0 1.8911775 0.959 0.739 0 G0S2
4 0 1.8649388 0.999 0.991 0 FABP4
5 0 1.8116877 0.585 0.147 0 ADIPOQ
6 0 1.5471742 0.557 0.322 0 ADIRF
7 0 1.4585314 0.785 0.411 0 CD36
8 0 1.4433467 0.732 0.159 0 PLIN4
9 0 1.4303713 0.840 0.236 0 GPD1
10 0 1.3479227 0.549 0.185 0 RBP4
11 0 1.3378702 0.809 0.164 0 PLIN1
12 0 1.3069709 0.696 0.165 0 FASN
13 0 1.2918998 0.988 0.850 0 DBI
14 0 1.2703044 0.887 0.391 0 PNPLA2
15 0 1.1849491 0.767 0.295 0 CHCHD10
16 0 1.0783518 0.937 0.533 0 CIDEC
17 0 1.0567199 0.922 0.546 0 HEBP2
248 0 1.0234040 0.447 0.210 0 MTRNR2L1
18 0 1.0196356 0.618 0.204 0 AGPAT2
19 0 0.9651879 0.784 0.235 0 ACACB
20 0 0.9617837 0.517 0.115 0 FADS1
21 0 0.9474505 0.667 0.230 0 ACSL1
22 0 0.8888489 0.591 0.115 0 UCP2
23 0 0.8751794 0.929 0.587 0 PLA2G16
24 0 0.8699395 0.620 0.230 0 INSIG1
25 0 0.8587624 0.964 0.767 0 CYB5A
26 0 0.8196034 0.451 0.067 0 LIPE
27 0 0.8080338 0.814 0.408 0 CYCS
28 0 0.7773532 0.428 0.060 0 DGAT2
29 0 0.7571747 0.377 0.070 0 GPAM
30 0 0.7543819 0.468 0.111 0 MRAP
31 0 0.7513995 0.505 0.084 0 PPP1R1A
32 0 0.7454391 0.908 0.662 0 COX7B
33 0 0.7285936 0.652 0.277 0 ACLY
34 0 0.7264040 0.725 0.307 0 SLC25A1
35 0 0.7081435 0.999 1.000 0 MT-CO2
279 0 0.7030135 0.211 0.024 0 LPL
36 0 0.6948749 0.509 0.072 0 AOC3
37 0 0.6604334 0.921 0.663 0 SLC25A5
38 0 0.6533328 0.407 0.077 0 FAM213A
39 0 0.6421343 0.766 0.377 0 CAV2
40 0 0.6316857 0.993 0.942 0 ALDOA
41 0 0.6294591 0.796 0.474 0 MPC2
42 0 0.6270537 0.993 0.946 0 COX7A2
253 0 0.6190016 0.257 0.040 0 PCK1
43 0 0.6176262 0.995 0.937 0 PRDX6
44 0 0.6120592 0.949 0.756 0 COX8A
45 0 0.6107311 0.969 0.819 0 ATP5G3
46 0 0.6091304 0.934 0.661 0 COL4A1
47 0 0.6052668 0.859 0.520 0 TIMM8B
48 0 0.6034987 0.441 0.064 0 ACSL5
49 0 0.6011568 0.994 0.939 0 UQCRQ
50 0 0.6008086 0.995 0.986 0 PTMA
51 0 0.5996341 0.881 0.560 0 ATP5B
52 0 0.5967354 0.582 0.297 0 FDPS
53 0 0.5899964 0.847 0.479 0 MDH1
54 0 0.5891652 0.466 0.066 0 AQP7
55 0 0.5844586 0.942 0.718 0 MRPL41
56 0 0.5776642 0.350 0.034 0 PRKAR2B
57 0 0.5753469 0.967 0.834 0 ATP5J
58 0 0.5748667 0.991 0.932 0 COX5B
59 0 0.5678075 0.397 0.059 0 LGALS12
60 0 0.5672789 0.967 0.842 0 UQCR10
61 0 0.5649240 0.986 0.924 0 UQCRH
62 0 0.5648477 0.779 0.389 0 ACADVL
63 0 0.5645716 0.815 0.428 0 CYC1
64 0 0.5564133 0.932 0.709 0 DDT
65 0 0.5562388 0.538 0.135 0 VKORC1L1
66 0 0.5543867 0.949 0.700 0 ETFB
67 0 0.5541594 0.881 0.598 0 COX5A
68 0 0.5497026 0.313 0.037 0 THRSP
69 0 0.5476794 0.773 0.352 0 NME1
70 0 0.5371121 0.925 0.684 0 NDUFC2
71 0 0.5361255 0.672 0.243 0 SHC1
72 0 0.5346643 0.609 0.204 0 ACO2
73 0 0.5278472 0.961 0.814 0 MGST3
74 0 0.5232081 0.881 0.557 0 COL4A2
75 0 0.5228482 0.491 0.093 0 FNDC4
76 0 0.5220889 0.856 0.570 0 PRDX2
77 0 0.5181163 0.472 0.123 0 HADH
78 0 0.5152906 0.903 0.618 0 DCXR
79 0 0.5029292 0.361 0.092 0 MVD
247 0 0.5026573 0.768 0.532 0 STOM
80 0 0.5014454 0.455 0.083 0 HK2
81 0 0.5009651 0.894 0.568 0 ENO1
82 0 0.4946480 0.448 0.070 0 ALDH1L1
83 0 0.4938111 0.674 0.277 0 MRPL12
84 0 0.4926468 0.537 0.168 0 CS
85 0 0.4918045 0.773 0.423 0 YWHAG
86 0 0.4911254 0.591 0.193 0 ISOC2
87 0 0.4884373 0.831 0.573 0 RPL22L1
88 0 0.4881559 0.865 0.549 0 AKR1C2
89 0 0.4870903 1.000 1.000 0 RPLP2
90 0 0.4870801 0.810 0.480 0 ELOVL5
91 0 0.4839989 0.472 0.090 0 ITGA7
92 0 0.4790120 0.988 0.954 0 SLC25A6
93 0 0.4766446 0.672 0.276 0 CSAD
94 0 0.4725353 0.749 0.343 0 MRPL23
95 0 0.4724549 0.997 0.988 0 MT-ATP6
96 0 0.4658894 0.999 0.998 0 MT-ND4
97 0 0.4657037 0.981 0.862 0 NDUFB2
252 0 0.4651636 0.341 0.071 0 HMGCS1
98 0 0.4641587 0.690 0.324 0 ECHS1
99 0 0.4596779 0.807 0.453 0 BCAP31
100 0 0.4572808 0.874 0.612 0 ATP5G1
101 0 0.4561524 0.834 0.489 0 GBE1
102 0 0.4561170 0.962 0.810 0 RTN4
103 0 0.4534031 0.866 0.608 0 COX14
104 0 0.4525655 0.819 0.501 0 NDUFA6
105 0 0.4521609 0.832 0.514 0 NDUFS8
106 0 0.4497413 0.739 0.392 0 RHOB
107 0 0.4479602 0.507 0.180 0 PDXK
324 0 0.4477185 0.283 0.100 0 HP
108 0 0.4469896 0.699 0.320 0 MTCH2
109 0 0.4462437 0.858 0.583 0 UQCRFS1
110 0 0.4434685 0.582 0.220 0 PPP1R14B
111 0 0.4432958 0.611 0.270 0 TSKU
112 0 0.4430642 0.944 0.805 0 ATP5D
301 0 0.4422965 0.319 0.127 0 CHI3L2
268 0 0.4420577 0.306 0.058 0 ACSS2
113 0 0.4419751 0.861 0.597 0 HSPE1
114 0 0.4368126 0.867 0.571 0 NDUFS6
115 0 0.4326943 0.457 0.109 0 FAH
116 0 0.4302819 0.387 0.062 0 SREBF1
117 0 0.4297691 0.531 0.166 0 FAM195A
269 0 0.4293498 0.944 0.774 0 APOE
337 0 0.4287948 0.273 0.125 0 C11orf96
118 0 0.4246917 0.785 0.499 0 EIF5A
119 0 0.4245221 0.904 0.652 0 TALDO1
120 0 0.4238569 0.898 0.670 0 TIMM13
121 0 0.4231312 0.561 0.230 0 PEMT
122 0 0.4225094 0.518 0.167 0 AIFM2
123 0 0.4210100 0.776 0.427 0 C1QBP
124 0 0.4208609 0.914 0.706 0 SLIRP
125 0 0.4199032 0.618 0.290 0 SH3PXD2A
126 0 0.4144307 0.904 0.699 0 MT-ND5
127 0 0.4129852 0.571 0.252 0 IDH1
128 0 0.4123038 0.999 0.993 0 MYL6
129 0 0.4114366 0.999 1.000 0 MT-CO3
130 0 0.4104477 0.697 0.375 0 COX17
131 0 0.4101654 0.492 0.128 0 CAMK1
132 0 0.4095750 0.974 0.893 0 UQCR11.1
133 0 0.4092634 0.992 0.935 0 NDUFS5
134 0 0.4089046 0.410 0.095 0 ERV3-1
135 0 0.4086221 0.963 0.801 0 ATP5J2
136 0 0.4079703 0.729 0.397 0 GCSH
137 0 0.4071789 0.959 0.814 0 USMG5
138 0 0.4067898 0.405 0.067 0 MESP1
139 0 0.4060720 0.879 0.627 0 AURKAIP1
277 0 0.4022523 0.320 0.081 0 NOTCH3
140 0 0.3993649 0.826 0.518 0 NDUFA3
141 0 0.3968682 0.763 0.444 0 ASPH
142 0 0.3944349 0.868 0.589 0 ECH1
143 0 0.3940340 0.515 0.171 0 ACO1
144 0 0.3933739 0.827 0.552 0 NDUFAB1
145 0 0.3929025 0.442 0.154 0 IDI1
318 0 0.3927756 0.723 0.416 0 RASD1
256 0 0.3917956 0.510 0.205 0 RDH5
146 0 0.3916896 0.963 0.824 0 LDHA
147 0 0.3910632 0.473 0.254 0 CDKN2C
148 0 0.3870365 0.723 0.379 0 HSPD1
149 0 0.3853895 0.399 0.104 0 RETSAT
150 0 0.3836226 0.990 0.953 0 ATP5L
259 0 0.3799294 0.334 0.060 0 DLAT
151 0 0.3788402 0.757 0.402 0 PHB
152 0 0.3765062 0.859 0.605 0 HSPA8
244 0 0.3754890 0.378 0.049 0 CLMN
153 0 0.3743367 0.889 0.824 0 MTRNR2L8
154 0 0.3740861 0.417 0.107 0 MMAB
295 0 0.3722141 0.286 0.066 0 HLA-DMA
155 0 0.3717264 0.993 0.975 0 CAV1
156 0 0.3706229 0.991 0.954 0 COX6B1
157 0 0.3699491 0.423 0.110 0 MRAS
158 0 0.3696316 0.926 0.733 0 NDUFB7
292 0 0.3673746 0.316 0.040 0 MLXIPL
159 0 0.3653028 0.918 0.729 0 ATP5I
299 0 0.3632776 0.388 0.159 0 TIMP4
160 0 0.3619079 0.914 0.718 0 COX6A1
296 0 0.3615633 0.390 0.129 0 MMD
161 0 0.3609143 0.999 0.997 0 MGST1
249 0 0.3591204 0.411 0.101 0 MKNK2
293 0 0.3576535 0.326 0.087 0 MSMO1
162 0 0.3569965 0.477 0.144 0 NR1H3
163 0 0.3568609 0.631 0.303 0 BOLA3
164 0 0.3557991 0.992 0.925 0 SAT1
246 0 0.3549774 0.478 0.149 0 GPC1
289 0 0.3541996 0.489 0.178 0 MME
285 0 0.3540137 0.420 0.149 0 HILPDA
165 0 0.3521484 0.899 0.659 0 RAN
166 0 0.3516043 0.631 0.286 0 UROS
167 0 0.3499098 0.713 0.385 0 G6PD
168 0 0.3484041 0.545 0.222 0 C20orf27
169 0 0.3470887 0.861 0.608 0 PRELID1
306 0 0.3466449 0.268 0.020 0 CEBPA
170 0 0.3439968 0.877 0.634 0 HSP90AA1
171 0 0.3428421 0.659 0.330 0 RTN3
250 0 0.3404516 0.479 0.183 0 HSD17B12
172 0 0.3399934 0.689 0.358 0 CISD3
345 0 0.3397997 0.377 0.150 0 IL17RE
173 0 0.3394396 0.743 0.402 0 HSD17B10
300 0 0.3390659 0.302 0.085 0 ME1
174 0 0.3387767 0.808 0.494 0 NHP2
262 0 0.3383261 0.691 0.455 0 FHL1
175 0 0.3369407 0.844 0.684 0 COX7A1
176 0 0.3358994 0.712 0.462 0 YWHAZ
177 0 0.3355317 0.864 0.602 0 C19orf70
178 0 0.3349688 0.951 0.799 0 PSMA7
281 0 0.3342182 0.444 0.153 0 DHCR24
179 0 0.3333487 0.993 0.985 0 ATP5E
287 0 0.3322712 0.488 0.214 0 TOB1
180 0 0.3321904 0.647 0.297 0 CAT
258 0 0.3311433 0.447 0.136 0 SLC25A4
181 0 0.3283443 0.999 1.000 0 MT-CO1
182 0 0.3282112 0.921 0.749 0 ATP5O
183 0 0.3281871 0.876 0.642 0 AKR1C3
184 0 0.3277222 0.789 0.497 0 LINC00116
185 0 0.3266503 0.666 0.368 0 TECR
186 0 0.3259517 0.996 0.977 0 COX7C
187 0 0.3248240 0.600 0.274 0 UQCRC1
188 0 0.3226131 0.474 0.138 0 PPARG
189 0 0.3205082 0.804 0.517 0 NDUFS7
257 0 0.3195467 0.590 0.266 0 EIF4EBP1
190 0 0.3193664 0.989 0.945 0 NDUFA4
275 0 0.3193467 0.415 0.149 0 LETM1
191 0 0.3179402 0.941 0.774 0 TPI1
390 0 0.3174487 0.491 0.305 0 HSD11B1
192 0 0.3169042 0.999 1.000 0 LGALS1
193 0 0.3164739 0.941 0.785 0 NDUFA1
194 0 0.3155912 0.645 0.332 0 MRPS12
245 0 0.3152373 0.544 0.239 0 ACAA2
278 0 0.3143023 0.478 0.213 0 GLRX5
195 0 0.3140140 0.889 0.699 0 C17orf89
307 0 0.3118525 0.665 0.512 0 MTRNR2L10
196 0 0.3106364 0.781 0.481 0 MDH2
197 0 0.3098151 0.682 0.351 0 HADHB
198 0 0.3095168 0.854 0.607 0 MINOS1
199 0 0.3081449 0.757 0.459 0 MLF2
200 0 0.3076045 0.999 0.998 0 MT-CYB
201 0 0.3075390 0.801 0.531 0 NME4
202 0 0.3073266 0.966 0.858 0 DYNLL1
203 0 0.3050834 0.633 0.335 0 DECR1
204 0 0.3048266 0.732 0.444 0 CALR
205 0 0.3035234 0.935 0.773 0 FKBP1A
206 0 0.3028480 0.767 0.465 0 VDAC1
276 0 0.3027719 0.447 0.163 0 FZD4
330 0 0.3017737 0.260 0.011 0 PDE3B
305 0 0.3002897 0.368 0.123 0 ACAT2
327 0 0.3000552 0.230 0.012 0 EPHA1-AS1
207 0 0.2992634 0.768 0.502 0 PGD
280 0 0.2988513 0.441 0.153 0 IMPAD1
208 0 0.2966906 0.894 0.680 0 ATP5A1
209 0 0.2961501 0.626 0.318 0 NDUFV3
210 0 0.2959820 0.894 0.705 0 NDUFB9
267 0 0.2954133 0.558 0.276 0 KIF5B
211 0 0.2950150 0.969 0.884 0 C14orf2
261 0 0.2942862 0.537 0.246 0 C20orf24
272 0 0.2941648 0.589 0.321 0 ASS1
212 0 0.2932942 0.725 0.433 0 LAMA4
213 0 0.2920553 0.772 0.482 0 UQCC2
304 0 0.2918269 0.382 0.124 0 TFRC
302 0 0.2913536 0.330 0.089 0 EBP
321 0 0.2913124 0.236 0.025 0 TM7SF2
286 0 0.2911367 0.527 0.230 0 ACTN1
326 0 0.2909249 0.373 0.145 0 MT-ND6
214 0 0.2882187 0.786 0.490 0 PFDN2
215 0 0.2867175 0.944 0.822 0 SRPX
283 0 0.2851152 0.433 0.141 0 DLD
216 0 0.2837749 0.727 0.399 0 ANXA6
328 0 0.2833065 0.910 0.737 0 AKR1C1
282 0 0.2826451 0.553 0.243 0 CD320
325 0 0.2815639 0.240 0.050 0 ACSF2
217 0 0.2806730 0.826 0.556 0 NDUFB8.1
312 0 0.2799768 0.319 0.095 0 LPIN1
251 0 0.2797438 0.659 0.372 0 ARL6IP1
218 0 0.2796333 0.883 0.687 0 CCDC85B
329 0 0.2794488 0.246 0.015 0 TUSC5
315 0 0.2779544 0.280 0.045 0 PTPRF
219 0 0.2779275 0.897 0.693 0 NDUFA2
335 0 0.2778049 0.488 0.308 0 MEST
298 0 0.2771925 0.425 0.151 0 NOP16
220 0 0.2765676 0.926 0.789 0 EIF3K
290 0 0.2761980 0.415 0.130 0 PDHA1
274 0 0.2750959 0.976 0.897 0 HSPB6
284 0 0.2750803 0.843 0.589 0 CD151
221 0 0.2749152 0.975 0.879 0 LDHB
222 0 0.2739205 0.747 0.444 0 NDUFAF3
223 0 0.2731452 0.912 0.725 0 ATOX1
260 0 0.2720072 0.722 0.484 0 CHP1
294 0 0.2719525 0.452 0.142 0 TSPAN14
265 0 0.2718098 0.647 0.339 0 PGK1
255 0 0.2700509 0.525 0.225 0 SLC25A39
297 0 0.2695807 0.428 0.188 0 PGM1
224 0 0.2693153 0.659 0.368 0 NDUFA8
273 0 0.2691674 0.503 0.202 0 PMVK
323 0 0.2685060 0.248 0.022 0 GPT2
225 0 0.2683308 0.690 0.389 0 UQCRC2
226 0 0.2680419 0.828 0.552 0 MRPL20
310 0 0.2678387 0.337 0.090 0 RP1-193H18.3
313 0 0.2648278 0.400 0.146 0 ATP2B4
264 0 0.2640395 0.561 0.280 0 MKKS
270 0 0.2633008 0.608 0.318 0 PXDN
227 0 0.2628533 0.709 0.433 0 GHITM
243 0 0.2624123 0.627 0.310 0 ETFA
319 0 0.2619744 0.594 0.310 0 SRM
320 0 0.2611602 0.254 0.027 0 DGAT1
228 0 0.2609854 0.859 0.645 0 HIGD2A
229 0 0.2607847 0.625 0.325 0 TXNL4A
230 0 0.2605587 0.647 0.356 0 COA3
354 0 0.2602344 0.288 0.128 0 APOC1
308 0 0.2594917 0.534 0.290 0 AKR1B1
271 0 0.2593420 0.586 0.280 0 LSM4
231 0 0.2588614 0.712 0.412 0 DNPH1
309 0 0.2585350 0.288 0.046 0 SORT1
232 0 0.2580523 0.722 0.431 0 SRSF3
233 0 0.2547827 0.933 0.762 0 YWHAE
234 0 0.2542113 0.687 0.401 0 MRPL34
291 0 0.2537132 0.582 0.291 0 SERPINH1
314 0 0.2536344 0.422 0.178 0 APMAP
311 0 0.2534278 0.318 0.087 0 ALAS1
235 0 0.2533945 0.989 0.973 0 YBX1
236 0 0.2519216 0.795 0.517 0 PSMD8
263 0 0.2513121 0.554 0.245 0 TMEM141
237 0 0.2507870 0.932 0.767 0 NDUFB11
238 0 0.2501242 0.877 0.656 0 DRAP1

Top 80 markers for metabolic branch sorted on logFC.

plots_metabolic <- FeaturePlot(seurobj, features.plot=as.vector(markers_metabolic$gene[1:80]), nCol=4, cols.use=c('gray', 'blue'), no.legend=F, no.axes=T, do.return=T)
plots_metabolic_edited <- list()

for (p in names(plots_metabolic)){
  plots_metabolic_edited[[p]] <- plots_metabolic[[p]] + scale_color_gradient(name='Expr.', low='gray', high='blue', guide='colorbar') + theme(legend.title=element_text(size=9), legend.text=element_text(size=9), legend.key.height = unit(0.6, 'cm'), legend.key.width=unit(0.2, 'cm'))
}

grid_metabolic <- plot_grid(plotlist=plots_metabolic_edited, ncol=4)

#grid_1 <- plot_grid(plotlist=plots_metabolic_edited[1:28], ncol=4)
#grid_2 <- plot_grid(plotlist=plots_metabolic_edited[29:56], ncol=4)

#save_plot('figures/figures_paper/supplementary_figures/7_branch-marker-genes/markers_upper_branch_1-28.pdf', grid_1, base_height=16, base_width=12)
#save_plot('figures/figures_paper/supplementary_figures/7_branch-marker-genes/markers_upper_branch_29_56.pdf', grid_2, base_height=16, base_width=12)
#save_plot('figures/figures_paper/supplementary_figures/7_branch-marker-genes/markers_upper_branch_1-28.png', grid_1, base_height=16, base_width=12)
#save_plot('figures/figures_paper/supplementary_figures/7_branch-marker-genes/markers_upper_branch_29_56.png', grid_2, base_height=16, base_width=12)
grid_metabolic

Version Author Date
8187313 Pytrik Folkertsma 2019-05-07

ECM genes

markers_ecm <- markers[markers$avg_logFC < 0,]
markers_ecm <- markers_ecm[order(markers_ecm$avg_logFC),]
kable(markers_ecm) %>%
  kable_styling(bootstrap_options = "striped", full_width = F)
p_val avg_logFC pct.1 pct.2 p_val_adj gene
266 0.0e+00 -1.4736756 0.412 0.716 0.0000000 APOD
242 0.0e+00 -1.4203376 0.830 0.976 0.0000000 MGP
241 0.0e+00 -1.3868741 0.873 0.996 0.0000000 DCN
303 0.0e+00 -1.3067572 0.184 0.406 0.0000000 CTGF
347 0.0e+00 -1.1216422 0.145 0.310 0.0000000 IGF2
240 0.0e+00 -1.0912836 0.806 0.976 0.0000000 CCDC80
239 0.0e+00 -1.0449993 0.463 0.778 0.0000000 RP11-572C15.6
254 0.0e+00 -1.0051597 0.805 0.966 0.0000000 PLAC9
333 0.0e+00 -0.9779005 0.566 0.794 0.0000000 COL1A1
336 0.0e+00 -0.9359817 0.396 0.575 0.0000000 THBS1
338 0.0e+00 -0.9084909 0.460 0.750 0.0000000 CLDN11
332 0.0e+00 -0.8775692 0.555 0.783 0.0000000 MFAP4
389 0.0e+00 -0.8760161 0.751 0.878 0.0000000 IGFBP6
317 0.0e+00 -0.8697664 0.993 1.000 0.0000000 CST3
334 0.0e+00 -0.8672895 0.926 0.993 0.0000000 MFAP5
331 0.0e+00 -0.8357621 0.959 0.997 0.0000000 IFITM3
408 0.0e+00 -0.8253483 0.618 0.782 0.0000000 S100A4
376 0.0e+00 -0.7853804 0.914 0.974 0.0000000 IGFBP7
367 0.0e+00 -0.7825588 0.538 0.680 0.0000000 CLU
288 0.0e+00 -0.7712418 0.242 0.598 0.0000000 PDGFRA
349 0.0e+00 -0.7683252 0.548 0.752 0.0000000 LUM
357 0.0e+00 -0.7652085 0.600 0.779 0.0000000 JUNB
322 0.0e+00 -0.7645133 0.630 0.817 0.0000000 FBN1
355 0.0e+00 -0.7638235 0.503 0.691 0.0000000 CYR61
316 0.0e+00 -0.7348863 0.119 0.406 0.0000000 IFITM1
352 0.0e+00 -0.7113562 0.564 0.753 0.0000000 ZFP36
442 0.0e+00 -0.6984895 0.944 0.972 0.0000000 TIMP1
423 0.0e+00 -0.6952933 0.430 0.509 0.0000000 PTGDS
373 0.0e+00 -0.6893209 0.959 0.979 0.0000000 CALD1
362 0.0e+00 -0.6841868 0.160 0.311 0.0000000 DPT
382 0.0e+00 -0.6809188 0.458 0.607 0.0000000 CYP1B1
340 0.0e+00 -0.6752993 0.341 0.579 0.0000000 FBLN1
344 0.0e+00 -0.6714240 0.656 0.790 0.0000000 PDLIM2
417 0.0e+00 -0.6405352 0.828 0.901 0.0000000 FOS
359 0.0e+00 -0.6357936 0.612 0.797 0.0000000 EMP3
375 0.0e+00 -0.6328013 0.774 0.884 0.0000000 MFGE8
369 0.0e+00 -0.6291763 0.780 0.905 0.0000000 C1S
406 0.0e+00 -0.6249373 0.780 0.895 0.0000000 C1R
343 0.0e+00 -0.6079750 0.186 0.398 0.0000000 CTSK
420 0.0e+00 -0.6003065 0.189 0.324 0.0000000 PTX3
453 0.0e+00 -0.5965988 0.781 0.873 0.0000000 S100A13
346 0.0e+00 -0.5893658 0.141 0.371 0.0000000 OSR2
383 0.0e+00 -0.5867891 0.588 0.730 0.0000000 ZFP36L1
459 0.0e+00 -0.5793361 0.948 0.986 0.0000000 COL1A2
392 0.0e+00 -0.5782118 0.756 0.884 0.0000000 IFITM2
364 0.0e+00 -0.5639808 0.319 0.535 0.0000000 CRLF1
361 0.0e+00 -0.5632580 0.332 0.533 0.0000000 FGF7
372 0.0e+00 -0.5496012 0.320 0.467 0.0000000 LOX
366 0.0e+00 -0.5469600 0.075 0.218 0.0000000 CCL2
379 0.0e+00 -0.5426199 0.449 0.605 0.0000000 EFEMP1
404 0.0e+00 -0.5407585 0.522 0.655 0.0000000 TPM1
486 0.0e+00 -0.5395325 0.937 0.955 0.0000000 S100A10
413 0.0e+00 -0.5379888 0.662 0.775 0.0000000 TCEAL4
500 0.0e+00 -0.5376989 0.911 0.895 0.0000559 COL3A1
381 0.0e+00 -0.5313284 0.388 0.596 0.0000000 SNAI2
462 0.0e+00 -0.5215079 0.623 0.787 0.0000000 PPAP2B
440 0.0e+00 -0.5204705 0.705 0.778 0.0000000 CD59
368 0.0e+00 -0.5139881 0.233 0.432 0.0000000 PRRX1
370 0.0e+00 -0.5077050 0.278 0.468 0.0000000 DAB2
445 0.0e+00 -0.5052342 0.507 0.633 0.0000000 PRKCDBP
405 0.0e+00 -0.5044662 0.187 0.376 0.0000000 LINC00152
439 0.0e+00 -0.4980286 0.712 0.772 0.0000000 SPOCK1
393 0.0e+00 -0.4934709 0.250 0.423 0.0000000 PRSS23
371 0.0e+00 -0.4857833 0.326 0.521 0.0000000 YPEL3
398 0.0e+00 -0.4857524 0.505 0.638 0.0000000 PNRC1
339 0.0e+00 -0.4851785 0.098 0.312 0.0000000 FBLN5
412 0.0e+00 -0.4711892 0.371 0.514 0.0000000 AXL
350 0.0e+00 -0.4709351 0.147 0.345 0.0000000 VGLL3
416 0.0e+00 -0.4703532 0.182 0.350 0.0000000 MIR4435-1HG
475 0.0e+00 -0.4663342 0.852 0.866 0.0000000 C6orf48
476 0.0e+00 -0.4636693 0.813 0.814 0.0000000 TIMP2
387 0.0e+00 -0.4582122 0.284 0.472 0.0000000 OLFML3
448 0.0e+00 -0.4574269 0.670 0.764 0.0000000 CYBRD1
435 0.0e+00 -0.4524769 0.459 0.574 0.0000000 ARID5B
365 0.0e+00 -0.4514171 0.192 0.385 0.0000000 ABCA6
488 0.0e+00 -0.4489217 0.920 0.929 0.0000000 FN1
360 0.0e+00 -0.4488806 0.068 0.209 0.0000000 CTHRC1
395 0.0e+00 -0.4466219 0.252 0.411 0.0000000 TCF4
341 0.0e+00 -0.4444798 0.048 0.244 0.0000000 LSP1
456 0.0e+00 -0.4444236 0.543 0.661 0.0000000 TPM4
356 0.0e+00 -0.4361096 0.171 0.371 0.0000000 ISLR
385 0.0e+00 -0.4309001 0.308 0.477 0.0000000 SH3D19
380 0.0e+00 -0.4307388 0.288 0.450 0.0000000 ZEB1
407 0.0e+00 -0.4279312 0.454 0.583 0.0000000 DDR2
342 0.0e+00 -0.4275094 0.077 0.276 0.0000000 CD34
463 0.0e+00 -0.4251619 0.540 0.589 0.0000000 TXNRD1
450 0.0e+00 -0.4214083 0.475 0.574 0.0000000 ADD3
348 0.0e+00 -0.4208061 0.072 0.276 0.0000000 DEPTOR
495 0.0e+00 -0.4145258 0.624 0.677 0.0000023 RRAS
492 0.0e+00 -0.4097523 0.363 0.426 0.0000003 ADM
429 0.0e+00 -0.3997669 0.187 0.263 0.0000000 SERPINE2
474 0.0e+00 -0.3991944 0.497 0.602 0.0000000 ZFP36L2
399 0.0e+00 -0.3940235 0.255 0.392 0.0000000 SLIT3
446 0.0e+00 -0.3910049 0.485 0.555 0.0000000 DPYSL2
358 0.0e+00 -0.3892257 0.115 0.308 0.0000000 CALHM2
427 0.0e+00 -0.3852036 0.263 0.362 0.0000000 SEMA3C
374 0.0e+00 -0.3831644 0.153 0.322 0.0000000 ABCA8
478 0.0e+00 -0.3783351 0.535 0.587 0.0000000 WBP5
497 0.0e+00 -0.3740986 0.433 0.507 0.0000190 MARCKS
443 0.0e+00 -0.3740643 0.131 0.232 0.0000000 DKK1
422 0.0e+00 -0.3738312 0.304 0.446 0.0000000 TFPI
460 0.0e+00 -0.3735668 0.534 0.594 0.0000000 SMIM14
494 0.0e+00 -0.3719382 0.535 0.609 0.0000003 MXRA8
438 0.0e+00 -0.3666916 0.256 0.404 0.0000000 NDRG1
484 0.0e+00 -0.3661539 0.441 0.508 0.0000000 IL6ST
433 0.0e+00 -0.3625350 0.264 0.386 0.0000000 LHFP
386 0.0e+00 -0.3581875 0.134 0.287 0.0000000 FRMD6
430 0.0e+00 -0.3556367 0.183 0.260 0.0000000 USP53
485 0.0e+00 -0.3553073 0.996 1.000 0.0000000 TMSB4X
363 0.0e+00 -0.3473315 0.044 0.189 0.0000000 TNNT3
421 0.0e+00 -0.3472240 0.188 0.297 0.0000000 MYADM
470 0.0e+00 -0.3448129 0.375 0.491 0.0000000 C1orf21
468 0.0e+00 -0.3445678 0.160 0.251 0.0000000 CILP
409 0.0e+00 -0.3436946 0.145 0.274 0.0000000 TMEM59L
449 0.0e+00 -0.3428310 0.258 0.357 0.0000000 HCFC1R1
351 0.0e+00 -0.3420740 0.046 0.214 0.0000000 PTGIS
411 0.0e+00 -0.3412664 0.211 0.350 0.0000000 HSD17B11
461 0.0e+00 -0.3378705 0.375 0.446 0.0000000 SLC38A2
377 0.0e+00 -0.3364780 0.031 0.153 0.0000000 WISP2
444 0.0e+00 -0.3285126 0.301 0.408 0.0000000 FAM198B
403 0.0e+00 -0.3276626 0.150 0.287 0.0000000 BASP1
481 0.0e+00 -0.3271414 0.319 0.407 0.0000000 PPAP2A
400 0.0e+00 -0.3271168 0.125 0.245 0.0000000 BICC1
431 0.0e+00 -0.3245189 0.266 0.387 0.0000000 NEXN
487 0.0e+00 -0.3238307 0.332 0.401 0.0000000 ANKRD28
451 0.0e+00 -0.3236846 0.191 0.289 0.0000000 PPP1R15A
466 0.0e+00 -0.3210070 0.227 0.308 0.0000000 CBR3
432 0.0e+00 -0.3208090 0.114 0.217 0.0000000 SPON2
441 0.0e+00 -0.3113038 0.134 0.233 0.0000000 MIR24-2
469 0.0e+00 -0.3093493 0.203 0.306 0.0000000 GPNMB
418 0.0e+00 -0.3092838 0.130 0.232 0.0000000 RIN2
489 0.0e+00 -0.3077585 0.510 0.556 0.0000000 RAB31
447 0.0e+00 -0.3033854 0.161 0.247 0.0000000 SLC40A1
457 0.0e+00 -0.3024642 0.150 0.238 0.0000000 PROCR
473 0.0e+00 -0.3012332 0.178 0.257 0.0000000 EPHB6
388 0.0e+00 -0.2998950 0.039 0.149 0.0000000 IER3
424 0.0e+00 -0.2991122 0.132 0.246 0.0000000 SVEP1
391 0.0e+00 -0.2981124 0.077 0.211 0.0000000 ABCA9
452 0.0e+00 -0.2978345 0.188 0.278 0.0000000 CELF2
483 0.0e+00 -0.2975602 0.357 0.425 0.0000000 HTRA1
503 9.0e-07 -0.2941391 0.839 0.818 0.0206998 EID1
394 0.0e+00 -0.2932849 0.084 0.211 0.0000000 CTD-2369P2.2
482 0.0e+00 -0.2904967 0.275 0.374 0.0000000 SCARA5
496 0.0e+00 -0.2875948 0.890 0.892 0.0000065 RABAC1
384 0.0e+00 -0.2871373 0.987 0.998 0.0000000 PFDN5
397 0.0e+00 -0.2870688 0.984 0.987 0.0000000 RPS27L
396 0.0e+00 -0.2866403 0.987 0.992 0.0000000 S100A11
458 0.0e+00 -0.2865729 0.246 0.336 0.0000000 LY96
499 0.0e+00 -0.2849428 0.219 0.298 0.0000296 TUBA1A
402 0.0e+00 -0.2831726 0.970 0.970 0.0000000 COL6A2
437 0.0e+00 -0.2819146 0.975 0.991 0.0000000 GSN
493 0.0e+00 -0.2797459 0.802 0.763 0.0000003 MYL12A
419 0.0e+00 -0.2772346 0.122 0.241 0.0000000 TGIF1
471 0.0e+00 -0.2756794 0.244 0.315 0.0000000 DST
464 0.0e+00 -0.2755761 0.192 0.259 0.0000000 ARHGAP29
477 0.0e+00 -0.2749453 0.170 0.255 0.0000000 ADAMTS5
472 0.0e+00 -0.2723758 0.232 0.317 0.0000000 PLP2
415 0.0e+00 -0.2722957 0.105 0.210 0.0000000 KLF4
378 0.0e+00 -0.2716798 0.033 0.152 0.0000000 SGK1
490 0.0e+00 -0.2699287 0.321 0.387 0.0000001 KANK2
410 0.0e+00 -0.2698614 0.054 0.141 0.0000000 NR4A1
455 0.0e+00 -0.2671119 0.214 0.312 0.0000000 LPAR1
426 0.0e+00 -0.2669031 0.092 0.195 0.0000000 CLEC2B
436 0.0e+00 -0.2636003 0.116 0.213 0.0000000 PODN
414 0.0e+00 -0.2634092 0.077 0.187 0.0000000 FIBIN
467 0.0e+00 -0.2633527 0.209 0.288 0.0000000 IFI16
480 0.0e+00 -0.2611765 0.205 0.274 0.0000000 CHIC2
428 0.0e+00 -0.2609559 0.935 0.942 0.0000000 ADH1B
425 0.0e+00 -0.2584379 0.094 0.197 0.0000000 ITGBL1
454 0.0e+00 -0.2577790 0.140 0.224 0.0000000 CCNG2
498 0.0e+00 -0.2571086 0.682 0.672 0.0000224 JUN
401 0.0e+00 -0.2569772 0.945 0.943 0.0000000 H3F3B
501 2.0e-07 -0.2569092 0.273 0.369 0.0041113 CRISPLD2
504 1.4e-06 -0.2562880 0.847 0.815 0.0323345 LAMC1
353 0.0e+00 -0.2519629 0.996 1.000 0.0000000 RPS27
465 0.0e+00 -0.2519161 0.870 0.866 0.0000000 COL6A3
491 0.0e+00 -0.2517855 0.801 0.733 0.0000002 SEPT11
434 0.0e+00 -0.2510037 0.132 0.222 0.0000000 PLSCR4
502 2.0e-07 -0.2508395 0.670 0.664 0.0042143 VAMP5
479 0.0e+00 -0.2502025 0.217 0.289 0.0000000 TSPAN4

Top 60 ECM branch genes sorted on logFC.

plots_ecm <- FeaturePlot(seurobj, features.plot=as.vector(markers_ecm$gene[1:80]), nCol=4, cols.use=c('gray', 'blue'), no.legend=F, no.axes=T, do.return=T)
plots_ecm_edited <- list()

for (p in names(plots_ecm)){
  plots_ecm_edited[[p]] <- plots_ecm[[p]] + scale_color_gradient(name='Expr.', low='gray', high='blue', guide='colorbar') + theme(legend.title=element_text(size=9), legend.text=element_text(size=9), legend.key.height = unit(0.6, 'cm'), legend.key.width=unit(0.2, 'cm'))
}

grid_ecm <- plot_grid(plotlist=plots_ecm_edited, ncol=4)

#grid_1 <- plot_grid(plotlist=plots_ecm_edited[1:28], ncol=4)
#grid_2 <- plot_grid(plotlist=plots_ecm_edited[29:56], ncol=4)

#save_plot('figures/figures_paper/supplementary_figures/7_branch-marker-genes/markers_lower_branch_1-28.pdf', grid_1, base_height=16, base_width=12)
#save_plot('figures/figures_paper/supplementary_figures/7_branch-marker-genes/markers_lower_branch_29_56.pdf', grid_2, base_height=16, base_width=12)
#save_plot('figures/figures_paper/supplementary_figures/7_branch-marker-genes/markers_lower_branch_1-28.png', grid_1, base_height=16, base_width=12)
#save_plot('figures/figures_paper/supplementary_figures/7_branch-marker-genes/markers_lower_branch_29_56.png', grid_2, base_height=16, base_width=12)
grid_ecm

Version Author Date
8187313 Pytrik Folkertsma 2019-05-07 


sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Storage

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_0.8.0.1    kableExtra_1.1.0 knitr_1.22       Seurat_2.3.4    
[5] Matrix_1.2-17    cowplot_0.9.4    ggplot2_3.1.0   

loaded via a namespace (and not attached):
  [1] Rtsne_0.15          colorspace_1.4-1    class_7.3-15       
  [4] modeltools_0.2-22   ggridges_0.5.1      mclust_5.4.3       
  [7] rprojroot_1.3-2     htmlTable_1.13.1    base64enc_0.1-3    
 [10] fs_1.2.7            rstudioapi_0.10     proxy_0.4-23       
 [13] npsurv_0.4-0        flexmix_2.3-15      bit64_0.9-7        
 [16] mvtnorm_1.0-10      xml2_1.2.0          codetools_0.2-16   
 [19] splines_3.5.3       R.methodsS3_1.7.1   lsei_1.2-0         
 [22] robustbase_0.93-4   jsonlite_1.6        Formula_1.2-3      
 [25] workflowr_1.2.0     ica_1.0-2           cluster_2.0.7-1    
 [28] kernlab_0.9-27      png_0.1-7           R.oo_1.22.0        
 [31] readr_1.3.1         compiler_3.5.3      httr_1.4.0         
 [34] backports_1.1.3     assertthat_0.2.1    lazyeval_0.2.2     
 [37] lars_1.2            acepack_1.4.1       htmltools_0.3.6    
 [40] tools_3.5.3         igraph_1.2.4        gtable_0.3.0       
 [43] glue_1.3.1          reshape2_1.4.3      RANN_2.6.1         
 [46] Rcpp_1.0.1          trimcluster_0.1-2.1 gdata_2.18.0       
 [49] ape_5.3             nlme_3.1-137        iterators_1.0.10   
 [52] fpc_2.1-11.1        gbRd_0.4-11         lmtest_0.9-36      
 [55] xfun_0.5            stringr_1.4.0       rvest_0.3.3        
 [58] irlba_2.3.3         gtools_3.8.1        DEoptimR_1.0-8     
 [61] MASS_7.3-51.1       zoo_1.8-5           scales_1.0.0       
 [64] hms_0.4.2           doSNOW_1.0.16       parallel_3.5.3     
 [67] RColorBrewer_1.1-2  yaml_2.2.0          reticulate_1.11.1  
 [70] pbapply_1.4-0       gridExtra_2.3       rpart_4.1-13       
 [73] segmented_0.5-3.0   latticeExtra_0.6-28 stringi_1.4.3      
 [76] highr_0.8           foreach_1.4.4       checkmate_1.9.1    
 [79] caTools_1.17.1.2    bibtex_0.4.2        Rdpack_0.10-1      
 [82] SDMTools_1.1-221    rlang_0.3.2         pkgconfig_2.0.2    
 [85] dtw_1.20-1          prabclus_2.2-7      bitops_1.0-6       
 [88] evaluate_0.13       lattice_0.20-38     ROCR_1.0-7         
 [91] purrr_0.3.2         labeling_0.3        htmlwidgets_1.3    
 [94] bit_1.1-14          tidyselect_0.2.5    plyr_1.8.4         
 [97] magrittr_1.5        R6_2.4.0            snow_0.4-3         
[100] gplots_3.0.1.1      Hmisc_4.2-0         pillar_1.3.1       
[103] whisker_0.3-2       foreign_0.8-71      withr_2.1.2        
[106] fitdistrplus_1.0-14 mixtools_1.1.0      survival_2.43-3    
[109] nnet_7.3-12         tsne_0.1-3          tibble_2.1.1       
[112] crayon_1.3.4        hdf5r_1.1.1         KernSmooth_2.23-15 
[115] rmarkdown_1.12      grid_3.5.3          data.table_1.12.0  
[118] git2r_0.25.2        webshot_0.5.1       metap_1.1          
[121] digest_0.6.18       diptest_0.75-7      tidyr_0.8.3        
[124] R.utils_2.8.0       stats4_3.5.3        munsell_0.5.0      
[127] viridisLite_0.3.0