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diff --git a/Figures/Cohort/Cohort_figures.html b/Figures/Cohort/Cohort_figures.html
diff --git a/Figures/Cohort/Cohort_figures.md b/Figures/Cohort/Cohort_figures.md
@@ -1,7 +1,7 @@
 Cohort figure generation (Figure 1a,b and Extended Data Figure 1a)
 ================
 Erin Pleasance
-2024-03-02
+2024-02-16
 
 This is an R markdown used to generate figures describing the overall
 cohort.

diff --git a/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-1.png b/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-1.png
diff --git a/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-2.png b/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-2.png
diff --git a/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-3.png b/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-3.png
diff --git a/Figures/Fig1_Sequencing_Stats/sequencing_stats.html b/Figures/Fig1_Sequencing_Stats/sequencing_stats.html
diff --git a/Figures/Phasing/Phasing_figures.html b/Figures/Phasing/Phasing_figures.html
diff --git a/Figures/Phasing/Phasing_figures.md b/Figures/Phasing/Phasing_figures.md
@@ -1,7 +1,7 @@
 Phasing figures
 ================
 Katherine Dixon
-2024-03-02
+2024-02-16
 
 This is an R markdown used to generate figures describing phasing.
 

diff --git a/Figures/Phasing/Phasing_figures_files/figure-gfm/output-1.png b/Figures/Phasing/Phasing_figures_files/figure-gfm/output-1.png
diff --git a/Figures/Phasing/Phasing_figures_files/figure-gfm/output-2.png b/Figures/Phasing/Phasing_figures_files/figure-gfm/output-2.png
diff --git a/Figures/Phasing/Phasing_figures_files/figure-gfm/output-3.png b/Figures/Phasing/Phasing_figures_files/figure-gfm/output-3.png
diff --git a/Figures/Phasing/phasing-stats.pdf b/Figures/Phasing/phasing-stats.pdf
diff --git a/Figures/Phasing/phasing-stats.png b/Figures/Phasing/phasing-stats.png
diff --git a/Figures/ecDNA/Extended_data_ecDNA_A.html b/Figures/ecDNA/Extended_data_ecDNA_A.html
@@ -608,7 +608,7 @@ <h2 id="loading-in-required-packages">Loading in required packages</h2>
 <pre><code>## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
 ## ✔ dplyr     1.1.4     ✔ readr     2.1.5
 ## ✔ forcats   1.0.0     ✔ stringr   1.5.1
-## ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
+## ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
 ## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
 ## ✔ purrr     1.0.2     
 ## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──

diff --git a/Figures/ecDNA/Extended_data_ecDNA_A.md b/Figures/ecDNA/Extended_data_ecDNA_A.md
@@ -11,7 +11,7 @@ library(tidyverse)
     ## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
     ## ✔ dplyr     1.1.4     ✔ readr     2.1.5
     ## ✔ forcats   1.0.0     ✔ stringr   1.5.1
-    ## ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
+    ## ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
     ## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
     ## ✔ purrr     1.0.2     
     ## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──

diff --git a/Figures/ecDNA/Extended_data_ecDNA_B.html b/Figures/ecDNA/Extended_data_ecDNA_B.html
@@ -608,7 +608,7 @@ <h2 id="loading-in-required-packages">Loading in required packages</h2>
 <pre><code>## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
 ## ✔ dplyr     1.1.4     ✔ readr     2.1.5
 ## ✔ forcats   1.0.0     ✔ stringr   1.5.1
-## ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
+## ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
 ## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
 ## ✔ purrr     1.0.2     
 ## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──

diff --git a/Figures/ecDNA/Extended_data_ecDNA_B.md b/Figures/ecDNA/Extended_data_ecDNA_B.md
@@ -11,7 +11,7 @@ library(tidyverse)
     ## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
     ## ✔ dplyr     1.1.4     ✔ readr     2.1.5
     ## ✔ forcats   1.0.0     ✔ stringr   1.5.1
-    ## ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
+    ## ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
     ## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
     ## ✔ purrr     1.0.2     
     ## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──

diff --git a/Figures/ecDNA/Extended_data_ecDNA_C.html b/Figures/ecDNA/Extended_data_ecDNA_C.html
diff --git a/Figures/ecDNA/Extended_data_ecDNA_C.md b/Figures/ecDNA/Extended_data_ecDNA_C.md
@@ -11,7 +11,7 @@ library(tidyverse)
     ## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
     ## ✔ dplyr     1.1.4     ✔ readr     2.1.5
     ## ✔ forcats   1.0.0     ✔ stringr   1.5.1
-    ## ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
+    ## ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
     ## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
     ## ✔ purrr     1.0.2     
     ## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
@@ -43,11 +43,4 @@ survfit2(Surv(time, status) ~ ecDNA, data = Long_POG_df) %>%
   add_risktable() 
 ```
 
-    ## Warning in ggplot2::geom_blank(): All aesthetics have length 1, but the data has 152 rows.
-    ## ℹ Did you mean to use `annotate()`?
-    ## All aesthetics have length 1, but the data has 152 rows.
-    ## ℹ Did you mean to use `annotate()`?
-    ## All aesthetics have length 1, but the data has 152 rows.
-    ## ℹ Did you mean to use `annotate()`?
-
 ![](Extended_data_ecDNA_C_files/figure-gfm/unnamed-chunk-3-1.png)<!-- -->
diff --git a/Figures/ecDNA/Extended_data_ecDNA_C_files/figure-gfm/unnamed-chunk-3-1.png b/Figures/ecDNA/Extended_data_ecDNA_C_files/figure-gfm/unnamed-chunk-3-1.png
diff --git a/Figures/ecDNA/Extended_data_ecDNA_D.html b/Figures/ecDNA/Extended_data_ecDNA_D.html
diff --git a/Figures/ecDNA/Extended_data_ecDNA_D.md b/Figures/ecDNA/Extended_data_ecDNA_D.md
@@ -11,7 +11,7 @@ library(tidyverse)
     ## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
     ## ✔ dplyr     1.1.4     ✔ readr     2.1.5
     ## ✔ forcats   1.0.0     ✔ stringr   1.5.1
-    ## ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
+    ## ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
     ## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
     ## ✔ purrr     1.0.2     
     ## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──

diff --git a/Figures/ecDNA/Extended_data_ecDNA_D_files/figure-gfm/unnamed-chunk-3-1.png b/Figures/ecDNA/Extended_data_ecDNA_D_files/figure-gfm/unnamed-chunk-3-1.png
diff --git a/Figures/ecDNA/Fig_5G.html b/Figures/ecDNA/Fig_5G.html
diff --git a/Figures/ecDNA/Fig_5G.md b/Figures/ecDNA/Fig_5G.md
@@ -12,7 +12,7 @@ library(tidyverse)
     ## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
     ## ✔ dplyr     1.1.4     ✔ readr     2.1.5
     ## ✔ forcats   1.0.0     ✔ stringr   1.5.1
-    ## ✔ ggplot2   3.5.0     ✔ tibble    3.2.1
+    ## ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
     ## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
     ## ✔ purrr     1.0.2
 
@@ -273,11 +273,7 @@ patch <- (r@ggplot / u / t )
 patch
 ```
 
-    ## Warning: Removed 39224 rows containing missing values or values outside the scale range
-    ## (`geom_segment()`).
-
-    ## Warning: Removed 1 row containing missing values or values outside the scale range
-    ## (`geom_segment()`).
+    ## Warning: Removed 39225 rows containing missing values (`geom_segment()`).
 
     ## `geom_smooth()` using formula = 'y ~ x'