forked from drieslab/spatial-datasets
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathdata_file_creation_for_Giotto.R
111 lines (79 loc) · 4.75 KB
/
data_file_creation_for_Giotto.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
library(data.table)
## 2016 ##
# spatial transcriptomics
ST_OB_data_1 = list(
dataset = 'ST_OB1',
spatial_locs = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2016_ST_olfactory_bulb/cell_locations/Rep11_MOB_0_location.txt",
expr_matrix = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2016_ST_olfactory_bulb/count_matrix/Rep11_MOB_0_expr.txt",
metadata = c(NA)
)
ST_OB_data_2 = list(
dataset = 'ST_OB2',
spatial_locs = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2016_ST_olfactory_bulb/cell_locations/Rep12_MOB_0_location.txt",
expr_matrix = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2016_ST_olfactory_bulb/count_matrix/Rep12_MOB_0_expr.txt",
metadata = c(NA)
)
## 2018 ##
# codex
codex_spleen_data = list(
dataset = 'codex_spleen',
spatial_locs = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_codex_spleen/cell_locations/codex_BALBc_3_coord.txt",
expr_matrix = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_codex_spleen/count_matrix/codex_BALBc_3_expression.txt.gz",
metadata = c("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_codex_spleen/cell_locations/codex_BALBc_3_annotation.txt",
"https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_codex_spleen/cell_locations/cell_type_annotation.csv")
)
# cyCIF
cyCIF_PDAC_data = list(
dataset = 'cycif_PDAC',
spatial_locs = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_CyCIF_PDAC/cell_locations/cyCIF_PDAC_coord.txt",
expr_matrix = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_CyCIF_PDAC/count_matrix/cyCIF_PDAC_expression.txt.gz",
metadata = c("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_CyCIF_PDAC/cell_locations/cyCIF_PDAC_annot.txt")
)
# merfish
merfish_preoptic_data = list(
dataset = 'merfish_preoptic',
spatial_locs = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_merFISH_science_hypo_preoptic/cell_locations/merFISH_3D_data_cell_locations.txt",
expr_matrix = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_merFISH_science_hypo_preoptic/count_matrix/merFISH_3D_data_expression.txt.gz",
metadata = c(NA)
)
# osmfish
osmfish_SS_data = list(
dataset = 'osmfish_SS_cortex',
spatial_locs = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_osmFISH_SScortex/cell_locations/osmFISH_prep_cell_coordinates.txt",
expr_matrix = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_osmFISH_SScortex/count_matrix/osmFISH_prep_expression.txt",
metadata = c(NA)
)
# starmap
starmap_cortex_data = list(
dataset = 'starmap_3D_cortex',
spatial_locs = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_starmap_3D_cortex/cell_locations/STARmap_3D_data_cell_locations.txt",
expr_matrix = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_starmap_3D_cortex/count_matrix/STARmap_3D_data_expression.txt",
metadata = c(NA)
)
## 2019
# seqfish ss cortex
seqfish_SS_data = list(
dataset = 'seqfish_SS_cortex',
spatial_locs = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2019_seqfish_plus_SScortex/cell_locations/cortex_svz_centroids_coord.txt",
expr_matrix = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2019_seqfish_plus_SScortex/count_matrix/cortex_svz_expression.txt",
metadata = c("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2019_seqfish_plus_SScortex/cell_locations/cortex_svz_centroids_annot.txt")
)
# seqfish OB
seqfish_OB_data = list(
dataset = 'seqfish_OB',
spatial_locs = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2019_seqfish_plus_olfactory_bulb/cell_locations/OB_centroids_coord.txt",
expr_matrix = "https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2019_seqfish_plus_olfactory_bulb/count_matrix/OB_expression.txt",
metadata = c("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2019_seqfish_plus_olfactory_bulb/cell_locations/OB_centroids_annot.txt")
)
# create datasets.txt
# need to be placed in /extdata directory of Giotto package
datasets = as.data.table(rbind(ST_OB_data_1,
ST_OB_data_2,
codex_spleen_data,
cyCIF_PDAC_data,
starmap_cortex_data,
osmfish_SS_data,
merfish_preoptic_data,
seqfish_SS_data,
seqfish_OB_data), row.names = F)
fwrite(datasets, './datasets.txt', sep = '\t')