module load R/3.6.1;R

setwd("/share/dept_bbsr/Projects/Czerniecki_Brian/2923_Oncogene_Expression_2020/work/attempt4")

library(dplyr)
library(ggplot2)

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level         = c('TCGA-BLCA_nrm','TCGA-BLCA_pri',
                  'TCGA-BRCA_nrm','TCGA-BRCA_pri',
                  'TCGA-COAD_nrm','TCGA-COAD_pri',
                  'TCGA-ESCA_nrm','TCGA-ESCA_pri',
                  'TCGA-HNSC_nrm','TCGA-HNSC_pri',
                  'TCGA-LUAD_nrm','TCGA-LUAD_pri',
                  'TCGA-LUSC_nrm','TCGA-LUSC_pri',
                                  'TCGA-OV_pri',
                  'TCGA-PAAD_nrm','TCGA-PAAD_pri',
                  'TCGA-PRAD_nrm','TCGA-PRAD_pri',
                  'TCGA-SKCM_nrm','TCGA-SKCM_pri',
                  'TCGA-STAD_nrm','TCGA-STAD_pri');

level1        = c('TCGA-BLCA',
                  'TCGA-BRCA',
                  'TCGA-COAD',
                  'TCGA-ESCA',
                  'TCGA-HNSC',
                  'TCGA-LUAD',
                  'TCGA-LUSC',
                  'TCGA-OV',
                  'TCGA-PAAD',
                  'TCGA-PRAD',
                  'TCGA-SKCM',
                  'TCGA-STAD');

level2        = c('nrm','pri');


num           = 20
len           = length(level)
cols          = c(as.character(rep(num,len)))

inf           = "file3d_boxplot.csv"
rawdat        = read.csv(file=inf,header=F)
exp           = rawdat
exp[1:5,]
rownames(exp) = rawdat[,2]
colnames(exp) = c("type","sample","val","project","tissue")
exp$type      <- factor(exp$type, levels = level)
exp$project   <- factor(exp$project, levels = level1)
exp$tissue    <- factor(exp$tissue, levels = level2)
exp[1:5,]

title         = "HER3_expression";
otf           = paste(title,".pdf",sep="")

cols = c("#00ff40", "#ff4000", 
         "#00ff40", "#ff4000",
         "#00ff40", "#ff4000",
         "#00ff40", "#ff4000",
         "#00ff40", "#ff4000",
         "#00ff40", "#ff4000",
         "#00ff40", "#ff4000",
                    "#ff0000",
         "#00ff40", "#ff4000",
         "#00ff40", "#ff4000",
         "#00ff40", "#ff4000",
         "#00ff40", "#ff4000"
         )


exp1 = exp
exp1$type = gsub("TCGA-BLCA_nrm","Bladder(N)",exp1$type)
exp1$type = gsub("TCGA-BLCA_pri","Bladder(T)",exp1$type)
exp1$type = gsub("TCGA-BRCA_nrm","Breast(N)",exp1$type)
exp1$type = gsub("TCGA-BRCA_pri","Breast(T)",exp1$type)
exp1$type = gsub("TCGA-COAD_nrm","Colon(N)",exp1$type)
exp1$type = gsub("TCGA-COAD_pri","Colon(T)",exp1$type)
exp1$type = gsub("TCGA-HNSC_nrm","Head & Neck(N)",exp1$type)
exp1$type = gsub("TCGA-HNSC_pri","Head & Neck(T)",exp1$type)
exp1$type = gsub("TCGA-LUAD_nrm","Lung(N)",exp1$type)
exp1$type = gsub("TCGA-LUAD_pri","Lung(T)",exp1$type)
exp1$type = gsub("TCGA-LUSC_nrm","Lung Squamous(N)",exp1$type)
exp1$type = gsub("TCGA-LUSC_pri","Lung Squamous(T)",exp1$type)
exp1$type = gsub("TCGA-OV_nrm","Ovarian(N)",exp1$type)
exp1$type = gsub("TCGA-OV_pri","Ovarian(T)",exp1$type)
exp1$type = gsub("TCGA-PAAD_nrm","Pancreatic(N)",exp1$type)
exp1$type = gsub("TCGA-PAAD_pri","Pancreatic(T)",exp1$type)
exp1$type = gsub("TCGA-PRAD_nrm","Prostate(N)",exp1$type)
exp1$type = gsub("TCGA-PRAD_pri","Prostate(T)",exp1$type)
exp1$type = gsub("TCGA-SKCM_nrm","Skin(N)",exp1$type)
exp1$type = gsub("TCGA-SKCM_pri","Skin(T)",exp1$type)
exp1$type = gsub("TCGA-STAD_nrm","Stomach(N)",exp1$type)
exp1$type = gsub("TCGA-STAD_pri","Stomach(T)",exp1$type)
exp1$type = gsub("TCGA-ESCA_nrm","Esophageal(N)",exp1$type)
exp1$type = gsub("TCGA-ESCA_pri","Esophageal(T)",exp1$type)


title      = "HER3 Expression";
otf        = "HER3_expression3.pdf";
pdf(otf)
ggplot(exp1, aes(x=type, y=val,fill=tissue)) + 
ggtitle(title) + xlab("") + ylab("FPKM (log2)") + theme(plot.title = element_text(size=20,hjust = 0.5,face="bold")) +
geom_jitter(color=num,shape=num, position=position_jitter(0.2),size = 0.2) +           
geom_boxplot(position = "dodge",alpha = 0.2,outlier.alpha = 0.1,outlier.size = 0.1, width=0.5) +
theme(axis.text.y=element_text(size=15),axis.title=element_text(size=14,face="bold")) +
theme(axis.text.x=element_text(size=15,angle=90,hjust=1,face="bold")) +
theme(legend.position = "none",panel.background = element_blank()) +
theme(axis.line.x = element_line(color="black", size = 0.6),axis.line.y = element_line(color="black", size = 0.6)) +
scale_fill_manual(values = c("#00ff00", "#ff0000")
)
dev.off()

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