Hi, I need help in drawing the graphs by using the R. I have generated the graphs for genes by following code as but colours for each plot are not appeared in graph. In first code, I have generated the bocplot for 6 samples i want each sample should be in colored but all are black. same as for PC and volcano graph. I am very thank full some one resole my problem.
boxplot(gene_expr_data + 0.01, col = pData(bg_data)$Color, log= "y", las = 2, names = pData(bg_data)$ID, ylim = c(0.01, 1E9)) plot(pc$x[,1:2], pch = 21, bg = pData(bg_data)$Color, cex = 2, ylim = c(-100, 100), xlim = c(-100, 100), xlab = "PC1", ylab = "PC2", cex.lab = 1.4, cex.axis = 1.3) plot(-log10(pval) ~ log2(fc), data = results_genes, pch = 21, main = "Volcano plot of differentially expressed genes", xlab = "log2 Fold Change", ylab = "-log10(P Value)", bg = "darkgrey", xlim = c(-8, 8), ylim=c(0, 19), cex.lab = 1.3, cex.axis = 1.3)