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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",
"https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_CyCIF_PDAC/raw_data/canvas.png")
)
# 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("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_merFISH_science_hypo_preoptic/cell_locations/merFISH_3D_metadata.txt")
)
# 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("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_osmFISH_SScortex/raw_data/osmFISH_prep_cell_metadata.txt")
)
# 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")
)
# slideseq cerebellum
slideseq_cerebellum_data = list(
dataset = 'slideseq_cerebellum',
spatial_locs = "https://zenodo.org/record/4034228/files/BeadLocationsForR.csv",
expr_matrix = "https://zenodo.org/record/4034228/files/MappedDGEForR.csv",
metadata = c("https://zenodo.org/record/4034228/files/l1.cerebellum.cellID.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.cells.nonblood.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.cells.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.class.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.genes.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.txt")
)
## 2020
ST_SCC_data = list(
dataset = 'ST_SCC',
spatial_locs = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_1_spatial_locs.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_2_spatial_locs.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_3_spatial_locs.csv"),
expr_matrix = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_1_expression.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_2_expression.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_3_expression.csv"),
metadata = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/raw_data/GSM4284316_P2_ST_rep1.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/raw_data/GSM4284317_P2_ST_rep2.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/raw_data/GSM4284318_P2_ST_rep3.jpg")
)
# 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,
slideseq_cerebellum_data,
ST_SCC_data), row.names = F)
fwrite(datasets, './datasets.txt', sep = '\t')
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",
"https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_CyCIF_PDAC/raw_data/canvas.png")
)
# 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("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_merFISH_science_hypo_preoptic/cell_locations/merFISH_3D_metadata.txt")
)
# 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("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_osmFISH_SScortex/raw_data/osmFISH_prep_cell_metadata.txt")
)
# 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")
)
# slideseq cerebellum
slideseq_cerebellum_data = list(
dataset = 'slideseq_cerebellum',
spatial_locs = "https://zenodo.org/record/4034228/files/BeadLocationsForR.csv",
expr_matrix = "https://zenodo.org/record/4034228/files/MappedDGEForR.csv",
metadata = c("https://zenodo.org/record/4034228/files/l1.cerebellum.cellID.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.cells.nonblood.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.cells.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.class.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.genes.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.txt")
)
## 2020
ST_SCC_data = list(
dataset = 'ST_SCC',
spatial_locs = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_1_spatial_locs.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_2_spatial_locs.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_3_spatial_locs.csv"),
expr_matrix = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_1_expression.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_2_expression.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_3_expression.csv"),
metadata = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/raw_data/GSM4284316_P2_ST_rep1.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/raw_data/GSM4284317_P2_ST_rep2.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/raw_data/GSM4284318_P2_ST_rep3.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/raw_data/p2_metadata.rds",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/raw_data/scrna_expr.rds")
)
# 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,
slideseq_cerebellum_data,
ST_SCC_data), row.names = F)
fwrite(datasets, './datasets.txt', sep = '\t')
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",
"https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_CyCIF_PDAC/raw_data/canvas.png")
)
# 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("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_merFISH_science_hypo_preoptic/cell_locations/merFISH_3D_metadata.txt")
)
# 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("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_osmFISH_SScortex/raw_data/osmFISH_prep_cell_metadata.txt")
)
# 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")
)
# slideseq cerebellum ####
slideseq_cerebellum_data = list(
dataset = 'slideseq_cerebellum',
spatial_locs = "https://zenodo.org/record/4034228/files/BeadLocationsForR.csv",
expr_matrix = "https://zenodo.org/record/4034228/files/MappedDGEForR.csv",
metadata = c("https://zenodo.org/record/4034228/files/l1.cerebellum.cellID.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.cells.nonblood.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.cells.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.class.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.genes.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.txt")
)
## 2020 ####
# ST SCC ####
ST_SCC_data = list(
dataset = 'ST_SCC',
spatial_locs = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_1_spatial_locs.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_2_spatial_locs.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_3_spatial_locs.csv"),
expr_matrix = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_1_expression.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_2_expression.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_3_expression.csv"),
metadata = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/p2_metadata.rds",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/scrna_expr.rds",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/normalized_sc_matrix.RDS",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/cell_type_vector.RDS",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/sign_list.RDS",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/lowres_images/P2_1_0.0625.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/lowres_images/P2_2_0.0625.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/lowres_images/P2_3_0.0625.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/imgReg.zip",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/PairsLigRec.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,
slideseq_cerebellum_data,
ST_SCC_data), row.names = F)
fwrite(datasets, './datasets.txt', sep = '\t')
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",
"https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_CyCIF_PDAC/raw_data/canvas.png")
)
# 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("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_merFISH_science_hypo_preoptic/cell_locations/merFISH_3D_metadata.txt")
)
# 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("https://raw.githubusercontent.com/RubD/spatial-datasets/master/data/2018_osmFISH_SScortex/raw_data/osmFISH_prep_cell_metadata.txt")
)
# 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")
)
# slideseq cerebellum ####
slideseq_cerebellum_data = list(
dataset = 'slideseq_cerebellum',
spatial_locs = "https://zenodo.org/record/4034228/files/BeadLocationsForR.csv",
expr_matrix = "https://zenodo.org/record/4034228/files/MappedDGEForR.csv",
metadata = c("https://zenodo.org/record/4034228/files/l1.cerebellum.cellID.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.cells.nonblood.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.cells.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.class.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.genes.txt",
"https://zenodo.org/record/4034228/files/l1.cerebellum.txt")
)
## 2020 ####
# ST SCC ####
ST_SCC_data = list(
dataset = 'ST_SCC',
spatial_locs = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_1_spatial_locs.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_2_spatial_locs.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_3_spatial_locs.csv"),
expr_matrix = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_1_expression.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_2_expression.csv",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_3_expression.csv"),
metadata = c("https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/p2_metadata.rds",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/scrna_expr.rds",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/normalized_sc_matrix.RDS",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/cell_type_vector.RDS",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/sign_list.RDS",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/lowres_images/P2_1_0.0625.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/lowres_images/P2_2_0.0625.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/lowres_images/P2_3_0.0625.jpg",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/imgReg.zip",
"https://github.com/RubD/spatial-datasets/raw/master/data/2020_ST_SCC/PairsLigRec.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,
slideseq_cerebellum_data,
ST_SCC_data), row.names = F)
fwrite(datasets, './datasets.txt', sep = '\t')