Update plots for rebuttal.

recount.Rmd

@@ -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)) +