examples/01_EFG.R

In CBIIT-CGBB/scCorr: A graph-based k-partitioning approach for single-cell gene-gene correlation analysis

rm(list=ls());

pdf("1_EFG.pdf", 24, 8);
source('supp_func.R');
load("../data/01/00zero_dist.RData")
layout(matrix(c(1,2,3), nrow = 1, ncol = 3, byrow = TRUE));
par("mar"=c(7, 7, 7, 7));

f.s <- c(1000, 4000, 7000, 10000, 13000, 15973);
## gene number from 14do_simulation_num.R
num <- c(15719, 18612, 19775, 20488, 21014, 21430);
cols <- rainbow(10, alpha=0.8);
col2 <- cols[c(1,2,7,3,9,6)];

boxplot(out.f$out.s, col=cols[7], border=cols[7], cex.axis=2.3);
title(font.main = 1,main="21430 full genes", xlab="", ylab = "",pch=19, cex.main=3,cex.lab=2, cex.axis= 2.5);
title(ylab="% of Zero Value", line=4, cex.lab=4, family = "sans");
title(xlab="Number of Cells", line=4.5, cex.lab=4, family = "sans");
fig_label('E', pos='topleft',cex=5)

boxplot(out.f$out2, col=cols[7], border=cols[7], cex.axis=2.3);
title(font.main = 1,main="347 pathway genes", xlab="", ylab = "",pch=19, cex.main=3,cex.lab=2, cex.axis= 2.5);
title(ylab="% of Zero Value", line=4, cex.lab=4, family = "sans");
title(xlab="Number of Cells", line=4.5, cex.lab=4, family = "sans");
fig_label('F', pos='topleft',cex=5)

for (i in 1:length(f.s)){
  n    <- f.s[i];
  inff <- paste0("../data/01/n", n, ".RData");
  load(inff);
  dat <- t(out.s);
  dat <- dat/num[i];
  v   <- apply(dat, 2, mean);
  colnames(dat) <- 1:200;
  main <- paste0("Single cell #:", n)
  if (i == 1){
    plot(v, type="l", col=col2[i], lwd=6, main="",
         xlab="", ylab="",cex.main=3, cex.axis=2.5);
    title(ylab="% of Zero Value", line=4, cex.lab=4, family = "sans")
    title(xlab="Number of Merged Cells", line=4.5, cex.lab=4, family = "sans")
    legend("topright", legend=f.s, lwd=6, title="Cell Number", bty="n", col=col2, cex = 3.5);
  } else {
    points(v, type="l", col=col2[i], lwd=6)
  }
}
fig_label('G', pos='topleft',cex=5)

dev.off();