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plots.R
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50 lines (42 loc) · 2.28 KB
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gqs <- extract_gq(candidates_DP_GQ_BAM)[[1]]
ggpf <- rbind(data.frame(id = "M", GQ = gqs[,1]),
data.frame(id = "Noot", GQ = gqs[,2]),
data.frame(id = "Heineken", GQ = gqs[,3]))
ggab <- data.frame(allelic_balance = extract_allelic_balance(candidates_DP_GQ_BAM)[[1]])
ggdpgq_dp <- rbind(data.frame(id = "M", DP = dpgq_depths[[1]][,1]),
data.frame(id = "Noot", DP = dpgq_depths[[1]][,2]),
data.frame(id = "Heineken", DP = dpgq_depths[[1]][,3]))
ggdpgq_gq <- rbind(data.frame(id = "M", GQ = dpgq_gq[[1]][,1]),
data.frame(id = "Noot", GQ = dpgq_gq[[1]][,2]),
data.frame(id = "Heineken", GQ = dpgq_gq[[1]][,3]))
ggdpgq_ab <- data.frame(allelic_balance = extract_allelic_balance(candidates_DP_GQ)[[1]])
ggplot(ggdpgq_dp, aes(DP, fill = id)) + geom_histogram(position = "dodge") + theme_bw() +
theme(
text = element_text(size = 20),
legend.text = element_text(size = 10),
axis.text = element_text(size = 20),
legend.justification=c(0,0), legend.position=c(0.05,0.8))
ggplot(ggdpgq_gq, aes(GQ, fill = id)) + geom_histogram(position = "dodge") + theme_bw() +
theme(
text = element_text(size = 20),
legend.text = element_text(size = 10),
axis.text = element_text(size = 20),
legend.justification=c(0,0), legend.position=c(0.05,0.8))
ggplot(ggdpgq_ab, aes(allelic_balance)) + geom_histogram(binwidth = 0.05, fill = "white", color = "black") + theme_bw() +
theme(
text = element_text(size = 20),
legend.text = element_text(size = 10),
axis.text = element_text(size = 20),
legend.justification=c(0,0), legend.position=c(0.05,0.8))
ggplot(ggab, aes(allelic_balance)) + geom_histogram(binwidth = 0.05, fill = "white", color = "black") + theme_bw() +
theme(
text = element_text(size = 20),
legend.text = element_text(size = 10),
axis.text = element_text(size = 20),
legend.justification=c(0,0), legend.position=c(0.05,0.8))
ggplot(ggpf, aes (GQ, fill = id)) + geom_histogram(position = "dodge", binwidth = 4) + theme_bw() +
theme(
text = element_text(size = 20),
legend.text = element_text(size = 10),
axis.text = element_text(size = 20),
legend.justification=c(0,0), legend.position=c(0.05,0.8))