get pbg_metrics data frames
ingest_training_stats(
simba_ref,
gg_dirname = "graph0",
tr_output = "model",
jsonpath
)reference to simba module
character(1) the dirname specified for build_and_train_pbg, defaults to 'graph0'
character(1) the output specified for build_and_train_pbg defaults to 'model'
character(1) path to training_stats.json
a list with two data.frames of training statistics
# full run-based, commented out as too long
# p3k = get_10x3kpbmc_path(overwrite=TRUE) # allow repetition
# ref = simba_ref()
# pp = ref$read_h5ad(p3k)
# bb = basic_preproc(pp, simba_ref=ref)
# gg = build_and_train_pbg( bb, simba_ref=ref )
# ts = ingest_training_stats(ref)
# head(ts$df1)
#
# use archived pbg output
#
tpath = system.file(file.path("extdata", "pbg3k.tar.xz"), package="Simba4Bioc")
untar(tpath, exdir = tempdir())
#> Warning: '/bin/tar -xf '' -C '/home/vincent/TEMP/Rtmpf7vh4D'' returned error code 2
jsonpath = paste0(tempdir(), "/pbg/graph0/model/training_stats.json")
ts = ingest_training_stats(jsonpath=jsonpath)
#> Warning: cannot open file '/home/vincent/TEMP/Rtmpf7vh4D/pbg/graph0/model/training_stats.json': No such file or directory
#> Error in file(con, "r"): cannot open the connection
head(ts$df1)
#> Error in (function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "object of type 'closure' is not subsettable", call = ts$df1, object = function (data = NA, start = 1, end = numeric(), frequency = 1, deltat = 1, ts.eps = getOption("ts.eps"), class = if (nseries > 1) c("mts", "ts", "matrix", "array") else "ts", names = if (!is.null(dimnames(data))) colnames(data) else paste("Series", seq(nseries))) { if (is.data.frame(data)) data <- data.matrix(data) if (is.matrix(data)) { nseries <- ncol(data) ndata <- nrow(data) dimnames(data) <- list(NULL, names) } else { nseries <- 1 ndata <- length(data) } if (ndata == 0) stop("'ts' object must have one or more observations") if (missing(frequency)) frequency <- 1/deltat else if (missing(deltat)) deltat <- 1/frequency if (frequency > 1 && 0 < (d <- abs(frequency - round(frequency))) && d < ts.eps) frequency <- round(frequency) if (!missing(start)) start <- as.numeric(start) if (length(start) > 1L) { start <- start[1L] + (start[2L] - 1)/frequency } if (!missing(end)) end <- as.numeric(end) if (length(end) > 1L) { end <- end[1L] + (end[2L] - 1)/frequency } if (missing(end)) end <- start + (ndata - 1)/frequency else if (missing(start)) start <- end - (ndata - 1)/frequency if (start > end) stop("'start' cannot be after 'end'") cycles <- as.numeric((end - start) * frequency) if (abs(round(cycles) - cycles) > ts.eps * max(cycles, 1)) stop("'end' must be a whole number of cycles after 'start'") nobs <- floor(cycles + 1.01) if (nobs != ndata) data <- if (NCOL(data) == 1) { if (ndata < nobs) rep_len(data, nobs) else if (ndata > nobs) data[1L:nobs] } else { if (ndata < nobs) data[rep_len(1L:ndata, nobs), ] else if (ndata > nobs) data[1L:nobs, ] } attr(data, "tsp") <- c(start, end, frequency) if (!is.null(class) && class[[1]] != "none") attr(data, "class") <- class data }), class = c("notSubsettableError", "error", "condition"))): error in evaluating the argument 'x' in selecting a method for function 'head': object of type 'closure' is not subsettable