graphs plotong by R

Question

[fatimarasool135]

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)

[Fabio Marroni]

Can you post the output of the command head(pData(bg_data)$Color)?

As an alternative, you can use this command to use six colors for the boxplot: boxplot(gene_expr_data + 0.01, col = c("red","blue","green","yellow","brown","pink"), log= "y", las = 2, names = pData(bg_data)$ID, ylim = c(0.01, 1E9))

[fatimarasool135]

Hi Fabio, Thank you. code you gave me functional and it resolve my problem. but I am stuck for PC and volcano graph.same issue colours are not show in graphs.code for PC and volcano graph shown in above post.

I have run this commad. head(pData(bg_data)$Color) out put was NULL

[fatimarasool135]

Hi fabio, colours are not shown in PC graph and valcano graph. kindly set the code

[Fabio Marroni]

Hi Fatima, changing the colors of a volcano plot implies that you know which points you want to be of different colors. I refer you to some examples that may help you:

How to change colour of points in volcano plot by common genes?

https://stackoverflow.com/questions/46197561/different-colors-of-points-in-volcano-plot-using-r

[fatimarasool135]

Yes got it. Thanks . Now I want to extract the list of genes (significant results) having FDR <0.05 and FC > 10.0 or FC<0.10 from file which have all expressed genes. how can i do it ?

[Fabio Marroni]

Can you share the first couple of lines of the dataset including your genes, FC and FDR?

[fatimarasool135]

head subsetq.csv "GeneName","feature","id","fc","pval","qval","Drought_sensitive_G1","Drought_sensitive_G2","Drought_tolerant_G3","Drought_tolerant_G4","Drought_tolerant_G5","Drought_tolerant_G6" ".","gene","MSTRG.10469",0.329488903619917,0.00142832748896338,0.259910259261526,2.5003,2.232766,0.135729,0,0,0.190792 ".","gene","MSTRG.10698",0.241268839517611,0.000317188508969446,0.136790531924965,2.923064,3.810668,0,0,0,0 ".","gene","MSTRG.13119",0.352790048999932,0.000539677563831664,0.180199910439792,1.701282,2.229747,0,0,0,0 ".","gene","MSTRG.13337",0.681896653988615,0.00204281315386956,0.295375398034284,19.546333,15.836477,12.656379,13.152587,15.144008,12.34343 ".","gene","MSTRG.14016",0.25669290807353,0.00196804175129006,0.29428213874073,4.482871,4.906847,0.389837,0.673042,1.040834,0.530697

[fatimarasool135]

Hi Fabio, please reply me . awaiting.

[Fabio Marroni]

Hi Fatima, I guess you have read the file subsetq.csv as an R object (data.frame or something else). I would need to see the first couple of lines of that object to be able to help you.