I would like to layer the black colored points over the gray. Any suggestions on how to do this

[keyvals.colour <- ifelse(
  data[[1]] %in% Cell, 'black', 'gray')

keyvals.colour[is.na(keyvals.colour)] <- 'gray'
names(keyvals.colour)[keyvals.colour == 'gray'] <- 'NS'
names(keyvals.colour)[keyvals.colour == 'black'] <- 'Cell Cycle'



EnhancedVolcano(data,
                lab = F,
                x = 'log2FoldChange',
                y = 'padj',
                selectLab = geneset_final[[1]],
                #xlab = bquote(~Log[2]~ 'fold change'),
                title = 'IMR-32 BRM014 v. DMSO',
                subtitle = "Cell Cycle",
                pCutoff = F,
                FCcutoff = F,
                #pointSize = 2.5,
                pointSize = ifelse(
                  data[[1]] %in% Cell,1 , 0.5),
                labSize = 2.5,
                #shapeCustom = keyvals.shape,
                colCustom = keyvals.colour,
                colAlpha = ifelse(
                  data[[1]] %in% Cell,1.0 ,0.5),
                legendLabSize = 15,
                #legendPosition = 'right',
                legendIconSize = 5.0,
                #labFace = 'bold',
                #boxedLabels = T,
                drawConnectors = F,
                widthConnectors = 0.5,
                #colConnectors = 'grey50',
                gridlines.major = F,
                gridlines.minor = F,
                border = 'full',
                #borderWidth = 1.5,
                borderColour = 'black')

Hi,

To do this, you have to re-order your input data; so, data, in this case. You will basically have to re-order it such that the genes pertaining to black dots / points are plot last, i.e., they appear in the final rows of data.

Kevin