From aca04dec1cae56c4bf9faa3a0afb6e015500a688 Mon Sep 17 00:00:00 2001
From: aduvermy <arnaud.duvermy@ens-lyon.fr>
Date: Thu, 26 Oct 2023 16:18:46 +0200
Subject: [PATCH] Fix NOTE "no visible binding for global variable" linked to
ggplot2
---
CHANGELOG | 13 ++++++++++++-
NAMESPACE | 1 +
R/evaluate_dispersion.R | 3 ++-
R/identity_plot.R | 3 ++-
R/plot_metrics.R | 4 ++--
R/roc_plot.R | 4 ++--
dev/flat_full.Rmd | 14 ++++++++------
7 files changed, 29 insertions(+), 13 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 2d10b3b..e4ec350 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -13,4 +13,15 @@ To do:
- The identity plot's point shape has been modified, enhancing the visual clarity of comparisons between HTRfit and DESeq2 results.
- Similar to the identity plot, the dispersion plot also benefits from improved point shape, contributing to a more effective visual analysis.
- Add xlab/ylab to ROC plot
- - The vignette section now includes a new topic, "About mixed model evaluation".
\ No newline at end of file
+ - The vignette section now includes a new topic, "About mixed model evaluation".
+
+
+# v1.0.2 : R files reorganization, log file enhancement and versioning
+
+ - R files have been restructured to enhance clarity.
+ - The log file location has been relocated to the R temporary directory.
+ - A bug that was causing issues with writing the 'group' information in log files during model update has been fixed.
+ - Fix NOTE "no visible binding for global variable" linked to ggplot2
+ - Fix bug with packageVersion("HTRfit")
+
+
diff --git a/NAMESPACE b/NAMESPACE
index 97817f4..bd1c8e3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -162,6 +162,7 @@ importFrom(plotROC,geom_roc)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(rlang,":=")
+importFrom(rlang,.data)
importFrom(stats,anova)
importFrom(stats,as.formula)
importFrom(stats,cor)
diff --git a/R/evaluate_dispersion.R b/R/evaluate_dispersion.R
index a16f96a..f049271 100644
--- a/R/evaluate_dispersion.R
+++ b/R/evaluate_dispersion.R
@@ -103,6 +103,7 @@ extract_tmbDispersion <- function(list_tmb) {
#' @param eval_dispersion A data frame containing actual and inferred dispersion values.
#' @param ... Additional arguments to be passed to the ggplot2::aes function.
#' @importFrom ggplot2 ggplot geom_point aes geom_abline theme_bw ggtitle scale_x_log10 scale_y_log10
+#' @importFrom rlang .data
#' @return A ggplot2 scatter plot.
#'
#' @export
@@ -117,7 +118,7 @@ dispersion_plot <- function(eval_dispersion, ...) {
args <- lapply(list(...), function(x) if (!is.null(x)) ggplot2::sym(x))
p <- ggplot2::ggplot(eval_dispersion) +
- ggplot2::geom_point(ggplot2::aes(x = actual_dispersion, y = inferred_dispersion, !!!args), size = 3, alpha = 0.6) +
+ ggplot2::geom_point(ggplot2::aes(x = .data$actual_dispersion, y = .data$inferred_dispersion, !!!args), size = 3, alpha = 0.6) +
ggplot2::geom_abline(intercept = 0, slope = 1, lty = 3, col = 'red', linewidth = 1) +
ggplot2::theme_bw() +
ggplot2::ggtitle("Dispersion evaluation") +
diff --git a/R/identity_plot.R b/R/identity_plot.R
index 943704f..01b7ed9 100644
--- a/R/identity_plot.R
+++ b/R/identity_plot.R
@@ -10,6 +10,7 @@
#' @return A ggplot2 identity plot.
#'
#' @importFrom ggplot2 sym aes geom_point geom_abline facet_wrap theme_bw ggtitle scale_x_log10 scale_y_log10
+#' @importFrom rlang .data
#' @export
#' @examples
#' comparison_data <- data.frame(
@@ -24,7 +25,7 @@ identity_plot <- function(comparison_df, ...){
ggplot2::ggplot(comparison_df) +
- ggplot2::geom_point(ggplot2::aes(x = actual, y = estimate, !!!args), alpha = 0.6, size = 2) +
+ ggplot2::geom_point(ggplot2::aes(x = .data$actual, y = .data$estimate, !!!args), alpha = 0.6, size = 2) +
ggplot2::geom_abline(intercept = 0, slope = 1, lty = 3, col = 'red', linewidth = 1) +
ggplot2::facet_wrap(~description, scales = "free") +
ggplot2::theme_bw() +
diff --git a/R/plot_metrics.R b/R/plot_metrics.R
index 24fbb45..956e2de 100644
--- a/R/plot_metrics.R
+++ b/R/plot_metrics.R
@@ -44,7 +44,7 @@ subset_glance <- function(glance_df, focus){
#'
#' @importFrom reshape2 melt
#' @importFrom ggplot2 aes facet_wrap geom_histogram theme_bw theme ggtitle
-#'
+#' @importFrom rlang .data
#' @export
#'
#' @examples
@@ -59,7 +59,7 @@ metrics_plot <- function(list_tmb, focus = NULL) {
}
long_glance_df <- reshape2::melt(glance_df, variable.name = "metric")
p <- ggplot2::ggplot(long_glance_df) +
- ggplot2::geom_histogram(ggplot2::aes(x = value, col = metric, fill = metric)) +
+ ggplot2::geom_histogram(ggplot2::aes(x = .data$value, col = .data$metric, fill = .data$metric)) +
ggplot2::facet_wrap(~metric, scales = "free") +
ggplot2::theme_bw() +
ggplot2::theme(legend.position = 'null') +
diff --git a/R/roc_plot.R b/R/roc_plot.R
index 1745b02..2b9e063 100644
--- a/R/roc_plot.R
+++ b/R/roc_plot.R
@@ -48,7 +48,7 @@ getLabelExpected <- function(comparison_df, coeff_threshold, alt_hypothesis) {
#' @return A ggplot object representing the ROC curve plot.
#' @importFrom plotROC geom_roc
#' @importFrom ggplot2 ggtitle theme_bw aes sym xlab ylab
-#'
+#' @importFrom rlang .data
#' @examples
#' comparison_data <- data.frame(
#' geneID = c("gene1", "gene2", "gene3"),
@@ -72,7 +72,7 @@ roc_plot <- function(comparison_df, ...) {
args <- lapply(list(...), function(x) if (!is.null(x)) ggplot2::sym(x))
#comparison_df$isDE <- factor(comparison_df$isDE, levels= c(TRUE, FALSE))
- p <- ggplot2::ggplot(comparison_df, ggplot2::aes(d = !isDE , m = p.adj, !!!args )) +
+ p <- ggplot2::ggplot(comparison_df, ggplot2::aes(d = !.data$isDE , m = .data$p.adj, !!!args )) +
plotROC::geom_roc(n.cuts = 0, labels = FALSE) +
ggplot2::theme_bw() +
ggplot2::ggtitle("ROC curve") +
diff --git a/dev/flat_full.Rmd b/dev/flat_full.Rmd
index d634a49..0cd2506 100644
--- a/dev/flat_full.Rmd
+++ b/dev/flat_full.Rmd
@@ -3763,7 +3763,7 @@ subset_glance <- function(glance_df, focus){
#'
#' @importFrom reshape2 melt
#' @importFrom ggplot2 aes facet_wrap geom_histogram theme_bw theme ggtitle
-#'
+#' @importFrom rlang .data
#' @export
#'
#' @examples
@@ -3778,7 +3778,7 @@ metrics_plot <- function(list_tmb, focus = NULL) {
}
long_glance_df <- reshape2::melt(glance_df, variable.name = "metric")
p <- ggplot2::ggplot(long_glance_df) +
- ggplot2::geom_histogram(ggplot2::aes(x = value, col = metric, fill = metric)) +
+ ggplot2::geom_histogram(ggplot2::aes(x = .data$value, col = .data$metric, fill = .data$metric)) +
ggplot2::facet_wrap(~metric, scales = "free") +
ggplot2::theme_bw() +
ggplot2::theme(legend.position = 'null') +
@@ -3936,6 +3936,7 @@ extract_tmbDispersion <- function(list_tmb) {
#' @param eval_dispersion A data frame containing actual and inferred dispersion values.
#' @param ... Additional arguments to be passed to the ggplot2::aes function.
#' @importFrom ggplot2 ggplot geom_point aes geom_abline theme_bw ggtitle scale_x_log10 scale_y_log10
+#' @importFrom rlang .data
#' @return A ggplot2 scatter plot.
#'
#' @export
@@ -3950,7 +3951,7 @@ dispersion_plot <- function(eval_dispersion, ...) {
args <- lapply(list(...), function(x) if (!is.null(x)) ggplot2::sym(x))
p <- ggplot2::ggplot(eval_dispersion) +
- ggplot2::geom_point(ggplot2::aes(x = actual_dispersion, y = inferred_dispersion, !!!args), size = 3, alpha = 0.6) +
+ ggplot2::geom_point(ggplot2::aes(x = .data$actual_dispersion, y = .data$inferred_dispersion, !!!args), size = 3, alpha = 0.6) +
ggplot2::geom_abline(intercept = 0, slope = 1, lty = 3, col = 'red', linewidth = 1) +
ggplot2::theme_bw() +
ggplot2::ggtitle("Dispersion evaluation") +
@@ -5658,7 +5659,7 @@ getLabelExpected <- function(comparison_df, coeff_threshold, alt_hypothesis) {
#' @return A ggplot object representing the ROC curve plot.
#' @importFrom plotROC geom_roc
#' @importFrom ggplot2 ggtitle theme_bw aes sym xlab ylab
-#'
+#' @importFrom rlang .data
#' @examples
#' comparison_data <- data.frame(
#' geneID = c("gene1", "gene2", "gene3"),
@@ -5682,7 +5683,7 @@ roc_plot <- function(comparison_df, ...) {
args <- lapply(list(...), function(x) if (!is.null(x)) ggplot2::sym(x))
#comparison_df$isDE <- factor(comparison_df$isDE, levels= c(TRUE, FALSE))
- p <- ggplot2::ggplot(comparison_df, ggplot2::aes(d = !isDE , m = p.adj, !!!args )) +
+ p <- ggplot2::ggplot(comparison_df, ggplot2::aes(d = !.data$isDE , m = .data$p.adj, !!!args )) +
plotROC::geom_roc(n.cuts = 0, labels = FALSE) +
ggplot2::theme_bw() +
ggplot2::ggtitle("ROC curve") +
@@ -5822,6 +5823,7 @@ test_that("Counts plot is generated correctly", {
#' @return A ggplot2 identity plot.
#'
#' @importFrom ggplot2 sym aes geom_point geom_abline facet_wrap theme_bw ggtitle scale_x_log10 scale_y_log10
+#' @importFrom rlang .data
#' @export
#' @examples
#' comparison_data <- data.frame(
@@ -5836,7 +5838,7 @@ identity_plot <- function(comparison_df, ...){
ggplot2::ggplot(comparison_df) +
- ggplot2::geom_point(ggplot2::aes(x = actual, y = estimate, !!!args), alpha = 0.6, size = 2) +
+ ggplot2::geom_point(ggplot2::aes(x = .data$actual, y = .data$estimate, !!!args), alpha = 0.6, size = 2) +
ggplot2::geom_abline(intercept = 0, slope = 1, lty = 3, col = 'red', linewidth = 1) +
ggplot2::facet_wrap(~description, scales = "free") +
ggplot2::theme_bw() +
--
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