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morris-lab / Capybara_reproducibility

Reproducibility Repository for Capybara
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lsk_matrix RDS file is not present in Figure 3/Intermediates/LARRY State Fate Data #3

Open HM-Anas opened 1 month ago

HM-Anas commented 1 month ago

The lsk_matrix.Rds file seems to be missing from its specified location. This file is crucial for the analysis in the "Weinreb et al 2020 analysis.Rmd file", particularly in the construction of reference data for Day 4 and Day 6 cells. Can someone explain this or re upload it?

2) Selection of proper cell types and construct references


### Only take Day 4 and Day 6 cells for reference
lsk.day.4.6 <- lsk[which(lsk$Time.point %in% c(4,6)), ]
lsk.day.4.6 <- lsk.day.4.6[which(lsk.day.4.6$Cell.type.annotation != "Undifferentiated"), ]

lsk.day.6 <- lsk[which(lsk$Time.point %in% c(6)), ]
lsk.day.6 <- lsk.day.6[which(lsk.day.6$Cell.type.annotation != "Undifferentiated"), ]

lsk.in.vitro <- readRDS("~/Desktop/Reproducibility/Figure 3/Intermediates/LARRY State Fate Data/lsk_matrix.Rds")
ct.freq.d6 <- as.data.frame(table(lsk.day.6$Cell.type.annotation))

## remove the cell type with less than 30 cells
less.than.30.ct.d6 <- as.character(ct.freq.d6[which(ct.freq.d6$Freq <= 30), "Var1"])

lsk.day.6.sub <- lsk.day.6[-which(lsk.day.6$Cell.type.annotation %in% less.than.30.ct.d6), ]
lsk.in.vitro <- as.matrix(t(lsk.in.vitro[rownames(lsk.day.4.6),]))

lsk.day.6.sub.wo.meg <- lsk.day.6.sub[which(lsk.day.6.sub$Cell.type.annotation != "Meg"), ]
lsk.day.6.sub.wo.meg.lym <- lsk.day.6.sub.wo.meg[which(lsk.day.6.sub.wo.meg$Cell.type.annotation != "Lymphoid"), ]

reference.new.d6.no.meg.lym <- construct.high.res.reference(lsk.in.vitro[,rownames(lsk.day.6.sub.wo.meg.lym)], lsk.day.6.sub.wo.meg.lym, criteria = "Cell.type.annotation")

saveRDS(reference.new.d6.no.meg.lym, "03_new_lsk_ref_with_cells_over_30_wo_undiff_d6_no_meg_lym.Rds")
Raeddarabseh commented 1 week ago

Only take Day 4 and Day 6 cells for reference

lsk.day.4.6 <- lsk[which(lsk$Time.point %in% c(4,6)), ] lsk.day.4.6 <- lsk.day.4.6[which(lsk.day.4.6$Cell.type.annotation != "Undifferentiated"), ]

lsk.day.6 <- lsk[which(lsk$Time.point %in% c(6)), ] lsk.day.6 <- lsk.day.6[which(lsk.day.6$Cell.type.annotation != "Undifferentiated"), ]

lsk.in.vitro <- readRDS("~/Desktop/Reproducibility/Figure 3/Intermediates/LARRY State Fate Data/lsk_matrix.Rds") ct.freq.d6 <- as.data.frame(table(lsk.day.6$Cell.type.annotation))

remove the cell type with less than 30 cells

less.than.30.ct.d6 <- as.character(ct.freq.d6[which(ct.freq.d6$Freq <= 30), "Var1"])

lsk.day.6.sub <- lsk.day.6[-which(lsk.day.6$Cell.type.annotation %in% less.than.30.ct.d6), ] lsk.in.vitro <- as.matrix(t(lsk.in.vitro[rownames(lsk.day.4.6),]))

lsk.day.6.sub.wo.meg <- lsk.day.6.sub[which(lsk.day.6.sub$Cell.type.annotation != "Meg"), ] lsk.day.6.sub.wo.meg.lym <- lsk.day.6.sub.wo.meg[which(lsk.day.6.sub.wo.meg$Cell.type.annotation != "Lymphoid"), ]

reference.new.d6.no.meg.lym <- construct.high.res.reference(lsk.in.vitro[,rownames(lsk.day.6.sub.wo.meg.lym)], lsk.day.6.sub.wo.meg.lym, criteria = "Cell.type.annotation")

saveRDS(reference.new.d6.no.meg.lym, "03_new_lsk_ref_with_cells_over_30_wo_undiff_d6_no_meg_lym.Rds")

HM-Anas commented 1 week ago

lsk_matrix.Rds is not available anywhere