################################################################################
#' @keywords internal
'%+%' = function(a, b) paste0(a, b)
################################################################################
#' @import stringr
#' @export
setMethod(
"show", signature = "conc_table",
definition = function(object){
n.row = nrow(object)
n.col = ncol(object)
row.show = min(nrow(object), 8)
col.show = min(ncol(object), 6)
cat(str_pad(">>>>>> Concentration Table <<<<<<", 50, "left", " ") %+%
str_pad("\nconc_table()", 35, "right", " ") %+%
"[ " %+%
str_pad(n.row, 3, "left", " ") %+%
" features and " %+%
str_pad(n.col, 3, "left", " ") %+%
" samples ]\n\n" %+%
"Showing the first " %+%
row.show %+% " samples and " %+%
col.show %+% " features...\n\n")
methods::show(object[1:row.show, 1:col.show])
cat("\n")
cat("... " %+% str_pad(n.col-col.show, 3, "left", " ") %+%
" more samples\n")
cat("... " %+% str_pad(n.row-row.show, 3, "left", " ") %+%
" more features\n")
}
)
################################################################################
#' @export
setMethod(
"show", signature = "sample_table",
definition = function(object){
n.row = nrow(object)
n.col = ncol(object)
row.show = min(nrow(object), 8)
col.show = min(ncol(object), 6)
cat(str_pad(">>>>>> Sample Table <<<<<<", 45, "left", " ") %+%
str_pad("\nsample_table()", 28, "right", " ") %+%
"[ " %+%
str_pad(n.row, 3, "left", " ") %+%
" samples and " %+%
str_pad(n.col, 3, "left", " ") %+%
" sample variables ]\n\n" %+%
"Showing the first " %+%
col.show %+% " samples and " %+%
row.show %+% " sample variables...\n\n")
methods::show(object[1:row.show, 1:col.show])
cat("\n")
cat("... " %+% str_pad(n.row-row.show, 3, "left", " ") %+%
" more samples\n")
cat("... " %+% str_pad(n.col-col.show, 3, "left", " ") %+%
" more sample variables\n")
}
)
################################################################################
#' @export
setMethod(
"show", signature = "feature_data",
definition = function(object){
n.row = nrow(object)
n.col = ncol(object)
row.show = min(nrow(object), 8)
col.show = min(ncol(object), 6)
cat(str_pad(">>>>>> Feature Data <<<<<<", 48, "left", " ") %+%
str_pad("\nfeature_data()", 24, "right", " ") %+%
"[ " %+%
str_pad(n.row, 3, "left", " ") %+%
" features and " %+%
str_pad(n.col, 3, "left", " ") %+%
" feature variables ]\n\n" %+%
"Showing the first " %+%
row.show %+% " samples and " %+%
col.show %+% " features...\n\n")
methods::show(object[1:row.show, 1:col.show])
cat("\n")
cat("... " %+% str_pad(n.col-col.show, 3, "left", " ") %+%
" more features\n")
cat("... " %+% str_pad(n.row-row.show, 3, "left", " ") %+%
" more feature variables\n")
}
)
################################################################################
#' @export
setMethod(
"show", signature = "ExperimentData",
definition = function(object){
for(i in seq_along(object@.Data)){
cat(names(object)[i])
cat(":\n")
methods::show(object@.Data[[i]])
cat("\n")
}
}
)
################################################################################
#' @export
setMethod(
"show", signature = "MetabolomicsExperimentData",
definition = function(object){
cat(str_pad(">>>>>> Metabolomics Experiment Data <<<<<<", 51, "left", " "))
cat("\n\n")
slots = splat_object(object)
for(i in 1:length(slots)){
slot_name = gsub("_", " ", names(slots)[i])
slot_name = str_to_title(slot_name)
if(is.character(slots[[i]]) | is.numeric(slots[[i]])){
cat(slot_name %+% ": " %+% slots[[i]])
cat("\n")
}else if(is.data.frame(slots[[i]])){
cat(slot_name %+% ": a " %+% nrow(slots[[i]]) %+% " by " %+%
ncol(slots[[i]]) %+% " data frame")
}
}
}
)
#' @export
setMethod(
"show", signature = "LipidomicsExperimentData",
definition = function(object){
cat(str_pad(">>>>>> Lipidomics Experiment Data <<<<<<", 50, "left", " "))
cat("\n\n")
slots = splat_object(object)
for(i in 1:length(slots)){
slot_name = gsub("_", " ", names(slots)[i])
slot_name = str_to_title(slot_name)
if(is.character(slots[[i]]) | is.numeric(slots[[i]])){
cat(slot_name %+% ": " %+% slots[[i]])
cat("\n")
}else if(is.data.frame(slots[[i]])){
cat(slot_name %+% ": a " %+% nrow(slots[[i]]) %+% " by " %+%
ncol(slots[[i]]) %+% " data frame\n")
}
}
}
)
################################################################################
#' @keywords internal
setMethod(
"length", signature = "ExperimentData",
definition = function(x){
slots = splat_object(x)
return(length(slots))
}
)
################################################################################
#' @export
setMethod(
"show", signature = "mSet",
definition = function(object){
if(inherits(object@experiment_data, "ExperimentData")) {
warning("The experiment_data slot is a " %+% class(object) %+% "-class which is deprecated. Please convert it to a list.")
}
# conc_table
if(!is.null(object@conc_table)){
cat(
str_pad("conc_table():", 24, "right", " ") %+%
"[ " %+%
str_pad(ncol(object@conc_table), 3, "left", " ") %+%
" samples and " %+%
str_pad(nrow(object@conc_table), 3, "left", " ") %+%
" features ]\n"
)
}
# sample_table
# conc_table
if(!is.null(object@sample_table)){
cat(
str_pad("sample_table():", 24, "right", " ") %+%
"[ " %+%
str_pad(nrow(object@sample_table), 3, "left", " ") %+%
" samples and " %+%
str_pad(ncol(object@sample_table), 3, "left", " ") %+%
" sample variables ]\n"
)
}
# feature_data
if(!is.null(object@feature_data)){
cat(
str_pad("feature_data():", 24, "right", " ") %+%
"[ " %+%
str_pad(nrow(object@feature_data), 3, "left", " ") %+%
" features and " %+%
str_pad(ncol(object@feature_data), 3, "left", " ") %+%
" feature variables ]\n"
)
}
# experiment_data
if(!is.null(object@experiment_data)){
cat(
str_pad("experiment_data():", 24, "right", " ") %+%
"[ " %+%
str_pad(length(object@experiment_data), 3, "left", " ") %+%
" experiment attributes ]\n"
)
}
}
)
################################################################################
#' @export
setMethod(
"show", signature = "MetabolomicsSet",
definition = function(object){
cat(str_pad(">>>>>> Metabolomics Experiment <<<<<<", 50, "left", " "))
cat("\n")
callNextMethod()
}
)
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