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#' Internal function to create long data object from `mx_dataset` object
#'
#' @param mx_data `mx_dataset` object
#'
#' @importFrom magrittr %>%
#'
#' @return `data.frame` in long format
#' @noRd
get_long_data <- function(mx_data){
## mx_data should always have raw data
rdata = mx_data$data
rdata$table = "raw"
## check if normalized
if(!is.null(mx_data$norm_data)){
ndata = mx_data$norm_data
ndata$table = "normalized"
}
## check if otsu data
if(!is.null(mx_data$otsu_data)){
odata = mx_data$otsu_data
if(mx_data$otsu_table == "both"){
base_data = rbind(rdata,ndata)
rm(rdata,ndata)
} else if(mx_data$otsu_table == "normalized"){
base_data = ndata
rm(rdata,ndata)
} else{
base_data = rdata
rm(rdata)
}
}
## make it long
long_data = base_data %>%
tidyr::gather(mx_data$marker_cols,
key = "marker",
value="marker_value")
rm(base_data)
## create join on to match naming conventions
join_on = c("slide_id","marker","table")
names(join_on) = c(mx_data$slide_id,"marker","table")
## add otsu data
if(!is.null(odata)){
long_data = long_data %>%
dplyr::left_join(y = odata,
by = join_on)
rm(odata)
}
long_data
}
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