Phylogenetic tree comparison (core gene alignment)

tli14 · Aug 3, 2022 · 5860e3c · 5860e3c
1 parent 608ecf6
commit 5860e3c
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/R_code/Fig7.EF.core_gene_tree_compare.R → R_code/Fig6.core_gene_tree_compare.R b/R_code/Fig7.EF.core_gene_tree_compare.R → R_code/Fig6.core_gene_tree_compare.R
@@ -3,7 +3,7 @@ library(dplyr)
 library(ggplot2) 
 
 ## Load phylogenetic comparison data of E. coli.
-EC_group <- read.table(file = "R_code/Fig7.phylogenetic_tree/EC_10_groups_core_algn_ete.txt", sep = "\t" )
+EC_group <- read.table(file = "R_code/Fig6.phylogenetic_tree/EC_10_groups_core_algn_ete.txt", sep = "\t" )
 EC_group$V1 <- factor(EC_group$V1, levels=c("50cut", "99comp", "2.0cont"))
 
 ## The nRF values for 10 E. coli datasets. The y-axis range between 0 and 1.
@@ -22,7 +22,7 @@ plot_EC <- ggplot(data=EC_group,aes(x=V1, y=V2, group=V1, fill=V1))+
 
 plot_EC
 
-## The frequency of edges (for Figure S9.C). 
+## The frequency of edges (for Figure S13). 
 plot_EC_edges <- ggplot(data=EC_group,aes(x=V1, y=V3, group=V1, fill=V1)) +
   geom_violin(trim=TRUE)+
   geom_boxplot(width=0.1, fill="white")+