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Plot_NHEJ_results.R

+library(openxlsx)
+library(dplyr)
+library(ggplot2)
+library(openxlsx)
+
+full.t <- read.xlsx("NHEJ_Alleles_corr_thr0.2.xlsx")
+head(full.t)
+tt <- full.t %>% filter(is.na(Ref)) %>% group_by(Sample, Group, Treatment) %>% summarise(PercModif = sum(perc_reads))
+ttref <- full.t %>% filter(Ref == "*" &Group != "OT3_R1") %>% group_by(Sample, Group, Treatment) %>% summarise(PercRef = sum(perc_reads))
+tt <- merge(tt, ttref, by = c("Sample", "Group", "Treatment"), all = T)
+tt$Tot <- tt$PercModif + tt$PercRef
+tt$PercModif[is.na(tt$PercModif)] <- 0
+tt$Group <- factor(tt$Group, levels = c("A", "B1", "B2", "Tigit", "OT1", "OT2", "OT3", "OT4", "OT5", "OT6", "OT7", "OT8"))
+head(tt)
+
+
+p <- ggplot(tt, aes(x = Treatment, y = PercModif, color = Treatment)) +
+    theme_bw(base_size = 13) +
+    theme(axis.text.x = element_text(angle = 45, hjust = 1),
+          legend.position = "none") +
+    geom_jitter(size = 2, alpha = .6, width = .4) +
+    scale_color_brewer(palette = "Set1") +
+    ylab("Sum % Modif.") +
+    scale_y_continuous(n.breaks = 10) +
+    facet_grid(.~Group)
+p