setMethod(
f = "show",
signature = "mass_dataset",
definition = function(object) {
###check again
check_result = check_mass_dataset(
expression_data = object@expression_data,
sample_info = object@sample_info,
variable_info = object@variable_info
)
if (check_result != "all good.") {
cat(crayon::red(check_result, "\n"))
cat(crayon::red(
"You may changed the slots, try to use update_mass_dataset().\n"
))
}
cat(crayon::yellow(paste(rep("-", 20), collapse = ""), "\n"))
cat(crayon::green("massdataset version:", object@version, "\n"))
cat(crayon::yellow(paste(rep("-", 20), collapse = ""), "\n"))
cat(crayon::green("1.expression_data:"))
cat(
"[",
nrow(object@expression_data),
"x",
ncol(object@expression_data),
"data.frame]\n"
)
cat(crayon::green("2.sample_info:"))
cat("[",
nrow(object@sample_info),
"x",
ncol(object@sample_info),
"data.frame]\n")
if (nrow(object@sample_info) <= 5) {
sample_id <- object@sample_info$sample_id
} else{
sample_id <-
c(head(object@sample_info$sample_id, 3),"...",
tail(object@sample_info$sample_id, 2))
}
cat(nrow(object@sample_info), "samples:")
cat(sample_id)
cat("\n")
cat(crayon::green("3.variable_info:"))
cat(
"[",
nrow(object@variable_info),
"x",
ncol(object@variable_info),
"data.frame]\n"
)
if (nrow(object@variable_info) <= 5) {
variable_id <- object@variable_info$variable_id
} else{
variable_id <-
c(head(object@variable_info$variable_id, 3),"...",
tail(object@variable_info$variable_id, 2))
}
cat(nrow(object@variable_info), "variables:")
cat(variable_id)
cat("\n")
cat(crayon::green("4.sample_info_note:"))
cat(
"[",
nrow(object@sample_info_note),
"x",
ncol(object@sample_info_note),
"data.frame]\n"
)
cat(crayon::green("5.variable_info_note:"))
cat(
"[",
nrow(object@variable_info_note),
"x",
ncol(object@variable_info_note),
"data.frame]\n"
)
cat(crayon::green("6.ms2_data:"))
cat("[",
sum(unlist(lapply(object@ms2_data, function(x) {
length(unique(x@variable_id))
}))),
"variables x",
sum(unlist(lapply(object@ms2_data, function(x) {
length(unique(x@ms2_spectra))
}))),
"MS2 spectra]\n")
cat(crayon::yellow(paste(rep("-", 20), collapse = ""), "\n"))
cat(crayon::green("Processing information\n"))
if (.hasSlot(object = object, name = "process_info") &
length(object@process_info) != 0) {
process_info <- object@process_info
cat(crayon::green(length(process_info), "processings in total\n"))
if (length(process_info) > 5) {
cat(crayon::green("Latest 3 processings show\n"))
process_info <- tail(process_info, 3)
}
for (idx in seq_along(process_info)) {
cat(crayon::green(names(process_info)[idx], paste(rep("-", 10), collapse = ""), "\n"))
if (length(process_info[[idx]]) == 1) {
data.frame(
"Package" = process_info[[idx]]@pacakge_name,
"Function used" = process_info[[idx]]@function_name,
"Time" = process_info[[idx]]@time
) %>%
print()
} else{
data.frame(
"Package" = process_info[[idx]] %>% lapply(function(x)
x@pacakge_name) %>% unlist(),
"Function used" = process_info[[idx]] %>% lapply(function(x)
x@function_name) %>% unlist(),
"Time" = process_info[[idx]] %>% lapply(function(x)
as.character(x@time)) %>% unlist()
) %>%
print()
}
}
} else{
cat(crayon::red("There are no processing for your data.\n"))
}
}
)
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