colvec <- c("cornflowerblue", "brown3")
namevec <- c("HC (T0)", "SLE (T0)")

boxplot(y ~ group, col = colvec, xlab = "",
        ylab = "Percent Positive", main = plottitle,
        frame.plot = FALSE, outline = F, ylim = c(0, ymax),
        names = namevec, cex.axis = 0.9, cex.lab = 0.95, lwd = 0.5) 

box(bty="l")
set.seed(8)
y <- rnorm(200)
group <- sample(LETTERS[1:2], size = 200,
                replace = TRUE)
stripchart(y ~ group,
           pch = 16, vertical = TRUE, cex = 0.5, method = "jitter",
           col = adjustcolor("black", alpha = 0.7), add = TRUE)


# install.packages("ggplot2")
library(ggplot2)

# Data
set.seed(8)
y <- rnorm(200)
group <- sample(LETTERS[1:2], size = 200,
                replace = TRUE)
df <- data.frame(y, group)

# Box plot by group with jitter
ggplot(df, aes(x = group, y = y, colour = group)) + 
  geom_boxplot(outlier.shape = NA) + 
  scale_color_manual(values=c("red", "black"))+
  #scale_fill_manual(values=c("blue", "red"))+
  geom_jitter(aes(colour=group)) +
  xlab("")+
  theme(
    panel.background = element_rect(fill = "white", colour = "grey50"),
    legend.position = "none")

##### LN vs NLN

library(openxlsx)
a <- loadWorkbook('/Users/tushar/Desktop/Dxterity2/Dxterity41.xlsx')
sheetNames <- sheets(a)
a11<- read.xlsx('/Users/tushar/Desktop/Dxterity2/Dxterity41.xlsx', sheet=3)
#a11[21:40,1:7]
dim(a11)
colnames(a11)
rownames(a11)
which(colnames(a11)=="Timepoint")
### 7 to 40
row_hc<- which(a11[,7]==0 & a11[,4]=="SLE" & a11[,5]=="A")
row_A<-  which(a11[,7]==1 & a11[,4]=="SLE" & a11[,5]=="A")
length(row_hc)
length(row_A)
data_hc<- a11[c(row_hc),c(10,12:20)]
dim(data_hc)
data_NLN<- a11[c(row_hc),c(10,12:20)]
dim(data_NLN)
data_LN<- a11[c(row_A),c(10,12:20)]
dim(data_LN)
data_NLN_LN <- rbind(data_NLN, data_LN)
LN_cond<- factor(c(rep("No Lupus Nephritis",dim(data_NLN)[1]),
                   rep("Lupus Nephritis",dim(data_LN)[1])),
                 levels=c("No Lupus Nephritis", "Lupus Nephritis"))
Expression<- data_NLN_LN$Plasmablasts.Module

df2 <- data.frame(Expression, LN_cond)

# Box plot by group with jitter
p21<- ggplot(df2, aes(x = LN_cond, y = Expression, colour = LN_cond)) + 
  geom_boxplot() + 
  scale_color_manual(values=c("black", "red"))+
  #scale_fill_manual(values=c("blue", "red"))+
  geom_jitter(aes(colour=LN_cond)) +
  xlab("")+
  ylab("DxTerity IFN Module expression")+
  theme(
    panel.background = element_rect(fill = "white", colour = "grey50"),
    legend.position = "none")

pdf("/Users/tushar/Desktop/Dxterity2/Boxplot_Plasmablasts_LNvsNLN_v3.pdf", 5,5)
p21
dev.off()



#####  HC vs SLE

library(openxlsx)
a <- loadWorkbook('/Users/tushar/Desktop/Dxterity2/Dxterity41.xlsx')
sheetNames <- sheets(a)
a11<- read.xlsx('/Users/tushar/Desktop/Dxterity2/Dxterity41.xlsx', sheet=3)
a11[1:5,1:5]
dim(a11)
colnames(a11)
rownames(a11)
which(colnames(a11)=="Timepoint")
### 7 to 40
row_hc<- which(a11[,5]=="HC")
row_A<- which(a11[,5]=="A" & a11[,4]=="SLE")
length(row_hc)
length(row_A)
data_hc<- a11[c(row_hc),c(10,12:20)]
dim(data_hc)
data_NLN<- a11[c(row_hc),c(10,12:20)]
dim(data_NLN)
data_LN<- a11[c(row_A),c(10,12:20)]
dim(data_LN)
data_NLN_LN <- rbind(data_NLN, data_LN)
LN_cond<- c(rep("Healthy Control",dim(data_NLN)[1]), rep("SLE",dim(data_LN)[1]))
Expression<- data_NLN_LN$Plasmablasts.Module

df2 <- data.frame(Expression, LN_cond)

df2 <- data.frame(Expression, LN_cond)

# Box plot by group with jitter
p21<- ggplot(df2, aes(x = LN_cond, y = Expression, colour = LN_cond)) + 
  geom_boxplot() + 
  scale_color_manual(values=c( "black", "red"))+
  #scale_fill_manual(values=c("blue", "red"))+
  geom_jitter(aes(colour=LN_cond)) +
  xlab("")+
  ylab("DxTerity IFN Module expression")+
  theme(
    panel.background = element_rect(fill = "white", colour = "grey50"),
    legend.position = "none")

pdf("/Users/tushar/Desktop/Dxterity2/Boxplot_Plasmablasts_HCvsSLE_v3.pdf", 5,5)
p21
dev.off()

tapply(df2$Expression, df2$LN_cond, summary)
tapply(df2$Expression, df2$LN_cond, sd)