ManiNetCluster-Visualization/preprocess.R at main · Oafish1/ManiNetCluster-Visualization · GitHub

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### Bulk Data
# Load data
load("bulk1.RData")
load("bulk2.RData")
meta1 = sel.meta1
meta2 = sel.meta2
# mat1, meta1, mat2, meta2

# Vars
prefix = "data/LiScience2018/"
mat = mat1
meta = meta1

# Write Data
paste("Mat Dim:", dim(mat)[1], "x", dim(mat)[2], "  Meta Dim:", dim(meta)[1], "x", dim(meta)[2])
dir.create(prefix)
write.csv(mat, paste(prefix, "mat.csv", sep=""))
write.csv(meta, paste(prefix, "meta.csv", sep=""))

# Vars
prefix = "data/GordonNature2021/"
mat = mat2
meta = meta2

# Write Data
paste("Mat Dim:", dim(mat)[1], "x", dim(mat)[2], "  Meta Dim:", dim(meta)[1], "x", dim(meta)[2])
dir.create(prefix)
write.csv(mat, paste(prefix, "mat.csv", sep=""))
write.csv(meta, paste(prefix, "meta.csv", sep=""))


### Pseudo Data
load("sc2sc.small.RData")
meta1 = ps.meta1
meta2 = ps.meta2
# mat1, meta1, mat2, meta2

# Filter cell types for visual
for (i in 1:length(meta1$cellType)) {
  if (!(meta1$cellType[i] %in% c("EN", "IN", "IPC", "RG", "Mural")))
    meta1$cellType[i] = "Other"
}
for (i in 1:length(meta2$cellType)) {
  if (!(meta2$cellType[i] %in% c("EN", "IN", "IPC", "RG", "Mural")))
    meta2$cellType[i] = "Other"
}

# Misc
# write.csv(knn_ini, "corr.csv")

# Vars
prefix = "data/NowakowskiScience2017/"
mat = mat1
meta = meta1

# Write Data
paste("Mat Dim:", dim(mat)[1], "x", dim(mat)[2], "  Meta Dim:", dim(meta)[1], "x", dim(meta)[2])
dir.create(prefix)
write.csv(mat, paste(prefix, "mat.csv", sep=""))
write.csv(meta, paste(prefix, "meta.csv", sep=""))

# Vars
prefix = "data/KantonNature2019/"
mat = mat2
meta = meta2

# Write Data
paste("Mat Dim:", dim(mat)[1], "x", dim(mat)[2], "  Meta Dim:", dim(meta)[1], "x", dim(meta)[2])
dir.create(prefix)
write.csv(mat, paste(prefix, "mat.csv", sep=""))
write.csv(meta, paste(prefix, "meta.csv", sep=""))


### All Data
load("all.data.RData")
# human.data1, human.data2, human.data3
# human.meta1, human.meta2, human.meta3
# org.data1, org.data2
# org.meta1, org.meta2

### Works
# # Vars
# prefix = "data/NowakowskiScience2017/"
# mat = t(human.data1)
# meta = human.meta1
#
# # Write Data
# paste("Mat Dim:", dim(mat)[1], "x", dim(mat)[2], "  Meta Dim:", dim(meta)[1], "x", dim(meta)[2])
# dir.create(prefix)
# write.csv(mat, paste(prefix, "mat.csv", sep=""))
# write.csv(meta, paste(prefix, "meta.csv", sep=""))

# Vars
prefix = "data/BireyNature2017/"
mat = t(org.data1)
meta = org.meta1

# Write Data
paste("Mat Dim:", dim(mat)[1], "x", dim(mat)[2], "  Meta Dim:", dim(meta)[1], "x", dim(meta)[2])
dir.create(prefix)
write.csv(mat, paste(prefix, "mat.csv", sep=""))
write.csv(meta, paste(prefix, "meta.csv", sep=""))

### Doesn't work
# Vars
prefix = "data/TrevinoCell2021/"
mat = t(as.matrix(human.data2)) # This is problematic
meta = human.meta2

# Write Data
paste("Mat Dim:", dim(mat)[1], "x", dim(mat)[2], "  Meta Dim:", dim(meta)[1], "x", dim(meta)[2])
dir.create(prefix)
write.csv(mat, paste(prefix, "mat.csv", sep=""))
write.csv(meta, paste(prefix, "meta.csv", sep=""))

# Vars
prefix = "data/BhaduriNature2020Brain/"
mat = human.data3
meta = human.meta3

# Write Data
paste("Mat Dim:", dim(mat)[1], "x", dim(mat)[2], "  Meta Dim:", dim(meta)[1], "x", dim(meta)[2])
dir.create(prefix)
write.csv(mat, paste(prefix, "mat.csv", sep=""))
write.csv(meta, paste(prefix, "meta.csv", sep=""))

# Vars
prefix = "data/BhaduriNature2020Org/"
mat = org.data2
meta = org.meta2

# Write Data
paste("Mat Dim:", dim(mat)[1], "x", dim(mat)[2], "  Meta Dim:", dim(meta)[1], "x", dim(meta)[2])
dir.create(prefix)
write.csv(mat, paste(prefix, "mat.csv", sep=""))
write.csv(meta, paste(prefix, "meta.csv", sep=""))