我是从另一个论坛（https://www.biostars.org/p/268514/#268559）交叉发布的，在那儿我得到了有用的评论，但仍然对ggplot2的输出感到困惑。
我试图在圆上得到一个简单的黑色轮廓，但是我的代码现在给出了随机的颜色，并且似乎忽略了我的scale_colour_manual（values = cols）参数。当我运行以下代码时：
# creating color palette
> cols <- c("red" = "red", "orange" = "orange", "nonsignificant" = "darkgrey", "Increased" = "#00B2FF", "Decreased" = "#00B2FF")
# Make a basic ggplot2 object
> vol <- ggplot(data, aes(x = lfc, y = pval, color = color, labels=gene))
# inserting mnaual colors as per color pallette with term "scale_colour_manual(values = cols)" below
> vol +
ggtitle(label = "Volcano Plot", subtitle = "Colored by fold-change direction") +
geom_point(size = 2.5, alpha …