From 3ee8b946b817e7363e9665d290d7077ae777b5c9 Mon Sep 17 00:00:00 2001
From: rpalaganas <ryanpalaganas96@gmail.com>
Date: Thu, 28 Mar 2024 12:25:21 -0400
Subject: [PATCH 1/2] Plotting updates

Fixed small bug where plots would not display due to cowplot::get_legend() returning many components. Resolved ggplot2 warnings printed to console due to use of `stats$label` rather than `label`
---
 R/plotting.R            | 2 +-
 R/projectionDriveRfun.R | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/R/plotting.R b/R/plotting.R
index 31bbfe4..3f44a59 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -170,7 +170,7 @@ plotVolcano <- function(
   volcano <- ggplot(data = stats,
                     aes(x = mean_diff, y = -log10(welch_padj),
                         color = Color,
-                        label = stats$label)) +
+                        label = label)) +
     geom_vline(xintercept = c(FC, -FC), lty = "dashed") +
     geom_hline(yintercept = -log10(pvalue), lty = "dashed") +
     geom_point(na.rm = TRUE) +
diff --git a/R/projectionDriveRfun.R b/R/projectionDriveRfun.R
index 91dd4e2..3776320 100644
--- a/R/projectionDriveRfun.R
+++ b/R/projectionDriveRfun.R
@@ -340,9 +340,7 @@ projectionDriveR <- function(
                                 result$plt$weighted_differential_expression +
                                   theme(legend.position = "none"),
                                 ncol = 2L, align = "h")
-      legend <- cowplot::get_legend(result$plt$differential_expression +
-                                      guides(color = guide_legend(nrow = 1L)) +
-                                      theme(legend.position = "bottom"))
+      legend <- cowplot::get_plot_component(result$plt$differential_expression, "guide-box-bottom")
       plt <- cowplot::plot_grid(pltgrid, legend, ncol = 1L, rel_heights = c(1.0, 0.1))
       print(plt)
     }

From 7433cff5d41dcf5a1008d034949357cebba28957 Mon Sep 17 00:00:00 2001
From: rpalaganas <ryanpalaganas96@gmail.com>
Date: Thu, 28 Mar 2024 12:31:46 -0400
Subject: [PATCH 2/2] Update plotting.R

---
 R/plotting.R | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/R/plotting.R b/R/plotting.R
index 3f44a59..66f112c 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -355,9 +355,7 @@ pdVolcano <- function(
                                   vol_result$plt$weighted_differential_expression +
                                     theme(legend.position = "none"),
                                   ncol = 2L, align = "h")
-    legend <- cowplot::get_legend(vol_result$plt$differential_expression +
-                                    guides(color = guide_legend(nrow = 1L)) +
-                                    theme(legend.position = "bottom"))
+    legend <- cowplot::get_plot_component(result$plt$differential_expression, "guide-box-bottom")
     plt <- cowplot::plot_grid(pltgrid,
                               legend,
                               ncol = 1L,