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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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104
R/comparison.R
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@ -18,38 +18,38 @@
#'
#' @export
compare <- function(ranking, comparison_gene_ids) {
if (!inherits(ranking, "geposan_ranking")) {
stop("Invalid ranking. Use geposan::ranking().")
}
if (!inherits(ranking, "geposan_ranking")) {
stop("Invalid ranking. Use geposan::ranking().")
}
comparison_ranking <- ranking[gene %chin% comparison_gene_ids]
comparison_ranking <- ranking[gene %chin% comparison_gene_ids]
quantiles <- data.table(
quantile = c("0%", "25%", "50%", "75%", "100%"),
score = stats::quantile(comparison_ranking[, score]),
rank = stats::quantile(
comparison_ranking[, rank],
probs = seq(1, 0, -0.25)
),
percentile = stats::quantile(comparison_ranking[, percentile])
)
quantiles <- data.table(
quantile = c("0%", "25%", "50%", "75%", "100%"),
score = stats::quantile(comparison_ranking[, score]),
rank = stats::quantile(
comparison_ranking[, rank],
probs = seq(1, 0, -0.25)
),
percentile = stats::quantile(comparison_ranking[, percentile])
)
p_value <- stats::wilcox.test(
x = comparison_ranking[, score],
y = ranking[!gene %chin% comparison_gene_ids, score],
alternative = "greater"
)$p.value
p_value <- stats::wilcox.test(
x = comparison_ranking[, score],
y = ranking[!gene %chin% comparison_gene_ids, score],
alternative = "greater"
)$p.value
structure(
list(
quantiles = quantiles,
mean_score = comparison_ranking[, mean(score)],
mean_rank = comparison_ranking[, mean(rank)],
mean_percentile = comparison_ranking[, mean(percentile)],
p_value = p_value
),
class = "geposan_comparison"
)
structure(
list(
quantiles = quantiles,
mean_score = comparison_ranking[, mean(score)],
mean_rank = comparison_ranking[, mean(rank)],
mean_percentile = comparison_ranking[, mean(percentile)],
p_value = p_value
),
class = "geposan_comparison"
)
}
#' S3 method to print a comparison object.
@ -61,32 +61,32 @@ compare <- function(ranking, comparison_gene_ids) {
#'
#' @export
print.geposan_comparison <- function(x, ...) {
cat("geposan comparison:\n\n")
cat("geposan comparison:\n\n")
quantiles_formatted <- x$quantiles[, .(
"Quantile" = quantile,
"Score" = round(score, 3),
"Rank" = rank,
"Percentile" = paste0(
format(round(percentile * 100, 1), nsmall = 1),
"%"
)
)]
quantiles_formatted <- x$quantiles[, .(
"Quantile" = quantile,
"Score" = round(score, 3),
"Rank" = rank,
"Percentile" = paste0(
format(round(percentile * 100, 1), nsmall = 1),
"%"
)
)]
print(quantiles_formatted, row.names = FALSE)
print(quantiles_formatted, row.names = FALSE)
cat(sprintf(
paste0(
"\n Mean score: %.3f",
"\n Mean rank: %.1f",
"\n Mean percentile: %.1f%%",
"\n p-value for better scores: %.4f\n"
),
x$mean_score,
x$mean_rank,
x$mean_percentile * 100,
x$p_value
))
cat(sprintf(
paste0(
"\n Mean score: %.3f",
"\n Mean rank: %.1f",
"\n Mean percentile: %.1f%%",
"\n p-value for better scores: %.4f\n"
),
x$mean_score,
x$mean_rank,
x$mean_percentile * 100,
x$p_value
))
invisible(x)
invisible(x)
}