# # read-in data, with only Subject as char, others as numeric
# data <- 'data/Eramus.xlsx'
# dat <- read.xlsx(data, sheetIndex = 1,
# colClasses = (c('character',
# rep('numeric', 20)))) %>%
# as_tibble() %>%
# select(-contains('NA')) %>% # delete NA column which is used as delim
# drop_na() %>% # drop row without information
# # select useful column
# select(-c(2:4)) %>%
# select(Subject = 1, everything())
#
# # need to create new var panel first
# dat$panel = regmatches(dat$Subject,
# regexpr(dat$Subject,
# pattern = '(Panel(\\d+))',
# perl = T))
#
# # extract meaningful name to muate original Subject var
# dat$Subject = regmatches(dat$Subject,
# regexpr(dat$Subject,
# pattern = '(?U)(?<=\\d{2}_)[^_]+_[^_]+_[^_]+(?=_[[:alpha:]]{2})',
# perl = T))
#
# # transform the tibble into a long format, new columns to indicate FITC or APC
# dat.long <- dat %>% pivot_longer(cols = c('FITC', 'APC'),
# names_to = 'FITC or APC',
# values_to = 'intensity',
# )
#
# # re-transform the tibble into a wide format, use `FITC or APC`and panel
# #togather to create multiple columns
# dat.wide <- dat.long %>% pivot_wider(names_from = c(`FITC or APC`, panel),
# values_from = intensity
# )
#
# # summarize(average) all the columns grouped by Subject
# dat.tranformed <- dat.wide %>%
# group_by(Subject) %>%
# summarise_all(mean, na.rm = T) #%>%
# # mutate(
# # HNE = matches('X.FITC.A._9PR', ignore.case = T),
# # CD91 = matches('X.FITC.A._10Tcel', ignore.case = T),
# # `PD-1` = X.FITC.A._11PD1,
# # CD47 = rowSums(.[grep('X.FITC.A._12Ap', ignore.case = T),], na.rm = T),
# # EXO = X.FITC.A._13EV,
# # ###################
# # CD163 = X.APC.A._9PR,
# # CDD172a = X.APC.A._10Tcel,
# # CD36 = X.APC.A._11PD1,
# # FLICA = X.APC.A._12Ap,
# # `TIMP-1` = X.APC.A._13EV,
# # )
# # %>%
# # select(Subject, CD45, CD63, CD16, CD66b, CD33, HNE, CD91,
# # `PD-1`, CD47, EXO, CD163, CDD172a, CD36, FLICA, `TIMP-1`,
# # everything()
# # )
#
# # for FITC
# # 9PR HNE
# # 10Tcel CD91
# # 11PD1 PD-1
# # 12Ap CD47
# # 13EV EXO
#
# ## For APC
# # 9PR CD163
# # 10Tcel CDD172a
# # 11PD1 CD36
# # 12Ap FLICA
# # 13EV TIMP-1
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