#download the raw data from https://github.com/BushmanLab/HSC_diversity/blob/master/data/intSites.mergedSamples.collapsed.csv.gz which is the data repository for https://ashpublications.org/blood/article-abstract/doi/10.1182/blood.2019002350/441042/Clonal-tracking-in-gene-therapy-patients-reveals-a?redirectedFrom=fulltext
raw_six_data <- read.csv("inst/sample_data/SixE_etal/intSites.mergedSamples.collapsed.csv.gz")
raw_six_data %>%
dplyr::filter(patient == "WAS5") %>%
dplyr::mutate(new_col_id = paste0("m", timePointMonths, "_", cellType)) %>%
tidyr::pivot_wider(id_cols = posid, values_from = reads, names_from = new_col_id) %>%
as.data.frame -> raw_six_data_reads
rownames(raw_six_data_reads) <- raw_six_data_reads$posid
raw_six_data_reads$posid <- NULL
raw_six_data_reads[is.na(raw_six_data_reads)] <- 0
raw_six_data %>%
dplyr::filter(patient == "WAS5") %>%
dplyr::mutate(new_col_id = paste0("m", timePointMonths, "_", cellType)) %>%
tidyr::pivot_wider(id_cols = posid, values_from = estAbund, names_from = new_col_id) %>%
as.data.frame -> raw_six_data_estabundance
rownames(raw_six_data_estabundance) <- raw_six_data_estabundance$posid
raw_six_data_estabundance$posid <- NULL
raw_six_data_estabundance[is.na(raw_six_data_estabundance)] <- 0
colname_order <- c("m13_TCELLS", "m13_BCELLS", "m13_NKCELLS", "m13_GRANULOCYTES", "m13_MONOCYTES",
"m36_TCELLS", "m36_BCELLS", "m36_NKCELLS", "m36_GRANULOCYTES", "m36_MONOCYTES",
"m43_TCELLS", "m43_BCELLS", "m43_NKCELLS", "m43_GRANULOCYTES", "m43_MONOCYTES",
"m55_TCELLS", "m55_BCELLS", "m55_NKCELLS", "m55_GRANULOCYTES", "m55_MONOCYTES")
raw_six_data_estabundance <- raw_six_data_estabundance[,colname_order]
raw_six_data_reads <- raw_six_data_reads[,colname_order]
WAS5_metadata <- data.frame(SAMPLENAME = colnames(raw_six_data_estabundance),
months = rep(c(13, 36, 43, 55), each = 5),
celltype = rep(c("T", "B", "NK", "Gr", "Mo"), times = 4))
all(rownames(raw_six_data_estabundance) == rownames(raw_six_data_reads))
write.table(file = "inst/sample_data/SixE_etal/WAS5_reads.txt", raw_six_data_reads, sep = '\t', quote = FALSE)
write.table(file = "inst/sample_data/SixE_etal/WAS5_estabundance.txt", raw_six_data_estabundance, sep = '\t', quote = FALSE)
write.table(file = "inst/sample_data/SixE_etal/WAS5_metadata.txt", WAS5_metadata, sep = '\t', quote = FALSE, row.names = FALSE)
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