r - ggplot2 绘制黑色轮廓

Question

我从另一个论坛 (https://www.biostars.org/p/268514/#268559) 交叉发帖，在那里我得到了有用的评论，但仍然对 ggplot2 的输出感到困惑。

我试图在圆圈上画一个简单的黑色轮廓，但我的代码现在给出随机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 = 1, na.rm = T) +
  scale_colour_manual(values = cols) +
  theme_bw(base_size = 14) + 
  theme(legend.position = "right") + 
  xlab(expression(log[2]("VitD" / "Carrier"))) + 
  ylab(expression(-log[10]("FDR"))) + # Change Y-Axis label
  geom_hline(yintercept = 1, colour="#990000", linetype="dashed") + geom_vline(xintercept = 0.586, colour="#990000", linetype="dashed") + geom_vline(xintercept = -0.586, colour="#990000", linetype="dashed") + 
  scale_y_continuous(trans = "log1p") 

我用我定义的调色板得到了一张漂亮的图表:

接下来，我想为点添加边框，所以我只更改了 2 段代码。一开始，我使用“fill = color”而不是“color = color”制作基本的 ggplot 对象

> vol <- ggplot(data, aes(x = lfc, y = pval, fill = color, labels=gene))

然后我将“shape = 21, color = "black""添加到“geom_point”参数:

> vol +   
  ggtitle(label = "Volcano Plot", subtitle = "Colored by fold-change direction") +
  geom_point(size = 2.5, alpha = 1, na.rm = T, shape = 21, colour = "black") +
  scale_colour_manual(values = cols) +
  theme_bw(base_size = 14) + 
  theme(legend.position = "right") + 
  xlab(expression(log[2]("VitD" / "Carrier"))) + 
  ylab(expression(-log[10]("FDR"))) + l
  geom_hline(yintercept = 1, colour="#990000", linetype="dashed") + geom_vline(xintercept = 0.586, colour="#990000", linetype="dashed") + geom_vline(xintercept = -0.586, colour="#990000", linetype="dashed") + 
  scale_y_continuous(trans = "log1p") 

突然间我有了一个似乎是随机选择 5 种颜色的情节；如果我打印颜色:

print(cols)

red      orange         nonsignificant      Increased      Decreased 
"red"    "orange"      "darkgrey"           "#00B2FF"      "#00B2FF" 

调色板还在。

Answer 1

当您将 color = cols 更改为 fill = cols 时，您还应该将 scale_color_manual(...) 更改为 scale_fill_manual (...)