Hello,

Thank you Kevin for this amazing EnhancedVolcano package! The overall result looks great. There's just one thing I am having difficulties fine-tuning, which is the length/dimension of the connectors of gene labels. I've searched around and I found a couple posts on this but the functions suggested are not working. Could you please help me understand what I might be doing wrong?

When I set the length of connectors (lengthConnectors = unit(1, 'npc')), the only thing that changes is the size of the arrowhead, not the connector line itself. This function is described to control "Length (size) of the connector arrowheads". Which is why if I turn off the arrowheads (arrowheads = FALSE), then this function doesn't have any effect. I was able to tune the width of the connector line through (widthConnectors = 1), but not the actual length of the connector lines.

Is there any way I can achieve this?

resddsCPM.df <- as.data.frame(resddsCPM)
keyvals <- ifelse(resddsCPM$padj > 0.05, 'grey30',
          ifelse(resddsCPM$log2FoldChange < -1, 'firebrick3',
            ifelse(resddsCPM$log2FoldChange > 1, 'royalblue', 'grey30')))
names(keyvals)[keyvals == 'royalblue'] <- 'Up'
names(keyvals)[keyvals == 'grey30'] <- 'Non-DEG'
names(keyvals)[keyvals == 'firebrick3'] <- 'Down'

#Highlight Genes of Interest
selected = c("IL1B", "FGF5", "IL1A")
#Plot Volcano
enhvolc <- EnhancedVolcano(resddsCPM.df, x = "log2FoldChange", y = "padj", lab = resddsCPM.df$geneID,
                pCutoff = 0.05, FCcutoff = 1,
                title = NULL,
                subtitle = NULL,
                caption = NULL,
                xlab = bquote(~Log[2]~"(Fold Change)"),
                ylab = bquote(~-Log[10] ~ "(" * italic(P[adj]) * ")"),
                drawConnectors = TRUE,
                pointSize = 1.2,
                colAlpha = 0.5,
                colCustom = keyvals,
                arrowheads = FALSE,
                lengthConnectors = unit(1, 'npc'),
                xlim = c(-11, 11),
                ylim = c(0, -log10(10e-306)),
                selectLab = selected
                )
enhvolc

Thank you for your help!

Peter

Hey Peter,

If arrowheads = TRUE, then the length and other parameters are used in code chunks like this in EnhancedVolcano:

  if (arrowheads) {
    arr <- arrow(length = lengthConnectors,
      type = typeConnectors, ends = endsConnectors)
  } else {
    arr <- NULL
  }

https://github.com/kevinblighe/EnhancedVolcano/blob/master/R/EnhancedVolcano.R#L808-L809

It's then used via ggrepel in a block like this:

  plot <- plot + geom_text_repel(
    data = subset(toptable,
      toptable[[y]] < pCutoff &
        abs(toptable[[x]]) > FCcutoff),
    aes(label = subset(toptable,
      toptable[[y]] < pCutoff &
        abs(toptable[[x]]) > FCcutoff)[["lab"]]),
    xlim = c(NA, NA),
    ylim = c(NA, NA),
    size = labSize,
    segment.color = colConnectors,
    segment.size = widthConnectors,
    arrow = arr,
    colour = labCol,
    fontface = labFace,
    parse = parseLabels,
    na.rm = TRUE,
    direction = directionConnectors,
    max.overlaps = max.overlaps,
    min.segment.length = min.segment.length)

https://github.com/kevinblighe/EnhancedVolcano/blob/master/R/EnhancedVolcano.R#L814-L833

As such, it's all some dictated by how ggrepel uses these parameters.

I don't believe there has ever been a parameter that allows you to control exactly the length of the connectors. However, one parameter that may help is to set a minimum length for each connector via:

' @param min.segment.length When drawConnectors = TRUE, specifies the minimum

' length of the connector line segments

This is somewhat elaborated here on ggrepel's documentation: https://ggrepel.slowkow.com/articles/examples.html

Kevin