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Reindent code to use just two spaces

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This commit is contained in:
Elias Projahn 2022-05-26 12:42:19 +02:00
parent a1e6147466
commit c04b6337e9
17 changed files with 1583 additions and 1582 deletions
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88
R/analyze.R
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@ -18,54 +18,54 @@
#'
#' @export
analyze <- function(preset, progress = NULL, include_results = TRUE) {
if (!inherits(preset, "geposan_preset")) {
stop("Preset is invalid. Use geposan::preset() to create one.")
}
if (!inherits(preset, "geposan_preset")) {
stop("Preset is invalid. Use geposan::preset() to create one.")
}
if (is.null(progress)) {
progress_bar <- progress::progress_bar$new()
progress_bar$update(0.0)
if (is.null(progress)) {
progress_bar <- progress::progress_bar$new()
progress_bar$update(0.0)
progress <- function(progress_value) {
if (!progress_bar$finished) {
progress_bar$update(progress_value)
if (progress_value >= 1.0) {
progress_bar$terminate()
}
}
progress <- function(progress_value) {
if (!progress_bar$finished) {
progress_bar$update(progress_value)
if (progress_value >= 1.0) {
progress_bar$terminate()
}
}
}
}
progress_buffer <- 0.0
method_count <- length(preset$methods)
progress_buffer <- 0.0
method_count <- length(preset$methods)
method_progress <- function(progress_value) {
progress(progress_buffer + progress_value / method_count)
}
method_progress <- function(progress_value) {
progress(progress_buffer + progress_value / method_count)
}
scores <- data.table(gene = preset$gene_id)
results <- list()
scores <- data.table(gene = preset$gene_id)
results <- list()
for (method in preset$methods) {
method_results <- method$func(preset, method_progress)
for (method in preset$methods) {
method_results <- method$func(preset, method_progress)
scores <- merge(scores, method_results$scores, by = "gene")
setnames(scores, "score", method$id)
scores <- merge(scores, method_results$scores, by = "gene")
setnames(scores, "score", method$id)
results <- c(results, list(method_results))
results <- c(results, list(method_results))
progress_buffer <- progress_buffer + 1 / method_count
progress(progress_buffer)
}
progress_buffer <- progress_buffer + 1 / method_count
progress(progress_buffer)
}
structure(
list(
preset = preset,
scores = scores,
results = if (include_results) results else NULL
),
class = "geposan_analysis"
)
structure(
list(
preset = preset,
scores = scores,
results = if (include_results) results else NULL
),
class = "geposan_analysis"
)
}
#' Print an analysis object.
@ -77,14 +77,14 @@ analyze <- function(preset, progress = NULL, include_results = TRUE) {
#'
#' @export
print.geposan_analysis <- function(x, ...) {
cat("geposan analysis:\n\n")
print(x$preset)
cat("geposan analysis:\n\n")
print(x$preset)
cat("\n")
for (result in x$results) {
print(result)
cat("\n")
}
for (result in x$results) {
print(result)
cat("\n")
}
invisible(x)
invisible(x)
}