Commit a32bbea9 authored by Venkat Malladi's avatar Venkat Malladi

Update plots for rebuttal.

parent d4c04c6a
......@@ -153,6 +153,7 @@ dev.off()
parp1_pam.aov = aov(PARP1 ~ PAM,data=df_pd_tcag_gtex_pam)
summary(parp1_pam.aov)
## DDX21 and PAM
df_ddx21_PAM_tcag_gtex_summary <- summarySE(df_pd_tcag_gtex_pam, measurevar="DDX21", groupvars=c("PAM"))
p <- ggplot(df_ddx21_PAM_tcag_gtex_summary, aes(x = as.factor(PAM), fill= PAM)) +
......@@ -207,6 +208,49 @@ dev.off()
parp1_et.aov = aov(PARP1 ~ ER + Type ,data=df_et_tcag_gtex_er_type_summary)
summary(parp1_et.aov)
# Remove Solid Tissue Normal
df_et_tcag_gtex$Type[df_et_tcag_gtex$Type == 'Metastatic'] <- 'Primary Tumor'
df_et_tcag_gtex_cn <- df_et_tcag_gtex[df_et_tcag_gtex$Type != 'Solid Tissue Normal',]
# Seperate into Types for different genes
df_et_tcag_gtex_cn$PARP1 <- log2(df_et_tcag_gtex_cn$PARP1)
df_et_tcag_gtex_cn$DDX21 <- log2(df_et_tcag_gtex_cn$DDX21)
## PARP1 Type
df_et_tcag_gtex_cn_type_summary <- summarySE(df_et_tcag_gtex_cn, measurevar="PARP1", groupvars=c('Type'))
p <- ggplot(df_et_tcag_gtex_cn_type_summary, aes(x = as.factor(Type), fill= Type)) +
geom_boxplot(aes(
lower = PARP1 - se,
upper = PARP1 + se,
middle = PARP1,
ymin = PARP1 - 2*se,
ymax = PARP1 + 2*se),
stat = "identity",lwd=1.5) + geom_hline(yintercept = mean(df_et_tcag_gtex_cn$PARP1), linetype = 2) + labs(y="RPKM",x="Type") + theme_bw() + theme(panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.ticks=element_line(size=1))
jpeg('figures/PARP1_breast_correlation_TYPE_boxplot.jpg')
p
dev.off()
parp1_type.aov = aov(PARP1 ~ Type ,data=df_et_tcag_gtex_cn_type_summary)
summary(parp1_type.aov)
## DDX21 Type
df_et_tcag_gtex_cn_type_summary <- summarySE(df_et_tcag_gtex_cn, measurevar="DDX21", groupvars=c('Type'))
p <- ggplot(df_et_tcag_gtex_cn_type_summary, aes(x = as.factor(Type), fill= Type)) +
geom_boxplot(aes(
lower = DDX21 - se,
upper = DDX21 + se,
middle = DDX21,
ymin = DDX21 - 2*se,
ymax = DDX21 + 2*se),
stat = "identity",lwd=1.5) + geom_hline(yintercept = mean(df_et_tcag_gtex_cn$DDX21), linetype = 2) + labs(y="RPKM",x="Type") + theme_bw() + theme(panel.grid.major = element_blank(),panel.grid.minor = element_blank(),axis.ticks=element_line(size=1))
jpeg('figures/DDX21_breast_correlation_TYPE_boxplot.jpg')
p
dev.off()
ddx21_type.aov = aov(DDX21 ~ Type ,data=df_et_tcag_gtex_cn_type_summary)
summary(ddx21_type.aov)
## PHF8 and ER and Type
df_ddx21_et_tcag_gtex_er_type_summary <- summarySE(df_et_tcag_gtex_er_type_com, measurevar="DDX21", groupvars=c("ER",'Type'))
p <- ggplot(df_ddx21_et_tcag_gtex_er_type_summary, aes(x = as.factor(ER), fill= Type)) +
......
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