volcano plot display selected labels

Question

[biology_inform]

Hi all, With the code below I try to draw volcano plot but there is a small problem. The labels that I selected is not shown in the graph.

volc <- EnhancedVolcano(dgeList_cpm_filtered_gtf,
                        lab = dgeList_cpm_filtered_gtf$gene_name,
                        x = 'logFC',
                        y = 'PValue',
                        xlab = bquote(~Log[2]~ 'FC'),
                        selectLab = c('VCAM1','NCAM2','FGFR1',
                                      'NLGN1','FGF5','UGT2B7','AKR1C2','SPP1','NR1H4','ALDH1A1'),
                        pCutoff = 0.05,
                        FCcutoff = 2,
                        pointSize = 1,
                        labSize = 4.0,
                        xlim = c(-20, 20),

                        axisLabSize = 18,
                        colAlpha = 1,
                        legendLabels = c("NS", expression(log[2] ~ FC), "p-value", expression(p - value ~ and~ log[2] ~ FC)),
                        legendPosition = 'right',
                        legendLabSize = 12,
                        legendIconSize = 4.0,
                        drawConnectors = FALSE,
                        widthConnectors = 0.75,
                        col=c('gray59', 'springgreen3', 'deepskyblue1', 'tomato1'),
                        title = "",
                        subtitle = "")

How can I show all 10 selected points in the graph? Thanks in advance

Answer 1

[Kevin Blighe]

Hi, please can you do 2 things to resolve this:

• verify that all of the desired genes are in dgeList_cpm_filtered_gtf$gene_name

• use drawConnectors = TRUE

Kevin

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Olá, por favor pode fazer 2 coisas para resolver isto:

• verificar que todos os genes ficam parte de dgeList_cpm_filtered_gtf$gene_name
• use drawConnectors = TRUE

Kevin