Question: graphs plotong by R
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gravatar for fatimarasool135
12 days ago by
fatimarasool13530 wrote:

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)
rna-seq R • 132 views
ADD COMMENTlink modified 12 days ago by h.mon26k • written 12 days ago by fatimarasool13530
2

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))

ADD REPLYlink modified 11 days ago • written 11 days ago by Fabio Marroni2.3k

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

ADD REPLYlink modified 10 days ago • written 11 days ago by fatimarasool13530

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

ADD REPLYlink written 10 days ago by fatimarasool13530

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

ADD REPLYlink modified 10 days ago • written 10 days ago by Fabio Marroni2.3k

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 ?

ADD REPLYlink written 5 days ago by fatimarasool13530

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

ADD REPLYlink written 5 days ago by Fabio Marroni2.3k

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

ADD REPLYlink written 5 days ago by fatimarasool13530

Hi Fabio, please reply me . awaiting.

ADD REPLYlink written 4 days ago by fatimarasool13530

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.

ADD REPLYlink written 4 days ago by Fabio Marroni2.3k
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