library(Seurat)


##########################################################
####DOTPLOT WITH STATISTIC FROM LIVER####
# Create function
PlotStellare <- function(obs1=obs1, features1=features1, valueG="NewlablesG",
                         i="CD8 T cells", group.by0 ="Clonetype2.Group", controGroup="SIINFEKL", noCtrlvsAll=T){
  obs1 <- SetIdent(obs1, value = valueG)
  pa1 <- DotPlot(obs1, features = features1, idents = i, dot.scale=15, split.by = group.by0,
                 cols="RdBu", scale=T)+RotatedAxis()
  df1 <- pa1$data
  contro0<- paste0(i,"_",controGroup)
  a1 <- sub(paste0(i,"_"),"",unique(df1$id))
  
  dfcombo <- NULL
  for (ix in a1){if(ix!=controGroup){
    m.Combo <- FindMarkers(obs1, ident.1 = ix,ident.2=controGroup, group.by = group.by0,
                           subset.ident = i,features = features1,
                           min.pct=0.01, logfc.threshold=0, min.cells.feature=1, min.cells.group=1)
  }else{
    m.Combo <- FindMarkers(obs1, ident.1 = ix,                     group.by = group.by0,
                           subset.ident = i,features = features1,
                           min.pct=0.01, logfc.threshold=0, min.cells.feature=1, min.cells.group=1)
    if(noCtrlvsAll){m.Combo$p_val_adj <- 1}
  }
    m.Combo <- m.Combo[match(features1,rownames(m.Combo)),]
    m.Combo$ix <- ix
    dfcombo <- rbind(dfcombo,m.Combo)}
  
  df2 <- cbind(df1,dfcombo)
  data.frame(df2$id,df2$ix)
  df2$stars <-  ifelse(df2$p_val_adj< 0.001,"***",
                       ifelse(df2$p_val_adj< 0.01,"**",
                              ifelse(df2$p_val_adj< 0.05,"*","")))
  
  df2$id <- factor(x = df2$id, levels = paste0(i,"_",rev(a1)))
  
  a <- ggplot(df2, aes(y=id, x=features.plot, size=pct.exp ,color=avg.exp.scaled)) + 
    geom_point() +
    scale_size_area(max_size=15) +
    scale_colour_gradient2(low="blue",mid="darkgrey",high="darkred") +  #"#CCCCFF"
    labs(y='',x='')+
    geom_text(aes(label=stars,vjust=0.8),col="black",size=4)+
    theme_classic()+
    theme(axis.text.y = element_text(color = "Black"))+
    theme(axis.text.x = element_text(angle=45, hjust=1, color = "Black"))+
    theme(axis.line.x=element_line(color="Black"))+
    theme(axis.line.y=element_line(color="Black"))+
    ggtitle(paste0(unique(obs1$Tissue),".",i," vs ",controGroup))
  return(a)}


plotRadar <- function(i){
  ploTData<- rbind(max1,min1,get(i))
  id <- sub(".db","",i)
  radarchart(ploTData, title = id, pcol=colors_border, pfcol=colors_in, plwd=2, plty=1, cglcol="grey", cglty = 1, cglwd=0.8)
}  #function to plot radarplot