不均匀的颜色条，R ggplot2 scale_color_gradient

Question

我正在尝试使用 ggplot2 创建绘图，但颜色条不代表实际数据。剧情看起来不错。

这是我的数据

                                  KEGG_Pathway Count Ratio pval_adjusted
1                        Amino acid metabolism    67 11.67  1.231153e-14
2    Xenobiotics biodegradation and metabolism    31 11.07  4.492243e-06
3                      Carbohydrate metabolism    54  7.78  2.940591e-05
4         Metabolism of cofactors and vitamins    34  8.76  2.439616e-04
5                            Energy metabolism    23  9.58  1.488961e-03
6                        Nucleotide metabolism    13  8.39  1.285896e-01
7              Metabolism of other amino acids    15  7.94  1.255625e-01
8  Biosynthesis of other secondary metabolites    20  5.17  1.000000e+00
9     Metabolism of terpenoids and polyketides    13  3.27  1.000000e+00
10                            Lipid metabolism     9  2.77  1.000000e+00

还有代码：

data$KEGG_Pathway <- factor(data$KEGG_Pathway, levels = rev(data$KEGG_Pathway))

myPalette <- colorRampPalette(brewer.pal(9, "BrBG"))(7)

ggplot(data, aes(Count, KEGG_Pathway)) + geom_point(aes(color=pval_adjusted, size=Ratio)) +
  scale_colour_gradientn(colours = myPalette,
                         values = rescale(c(1.23e-14,4.49e-06,2.94e-05,2.44e-04,
                                            1.49e-03,1.29e-01,1.26e-01,1)), limits = c(1e-14,1)) +
  scale_size_area(breaks = seq(0,12, by=2)) + theme_bw()

情节看起来和我想要的完全一样。但是颜色条完全是疯狂的（我想要一个渐变条来显示我的向量值的限制，以及我调色板中的所有颜色，就像在here 中一样）：

我玩过 guide = "colorbar" 和 guide_colorbar() ，但它总是会产生这种效果。

Answer 1

具有对数刻度的颜色图可能是您问题的可接受解决方案：

data <- structure(list(id = 1:10, KEGG_Pathway = structure(c(1L, 10L, 
3L, 6L, 4L, 9L, 7L, 2L, 8L, 5L), .Label = c("Amino acid metabolism", 
"Biosynthesis of other secondary metabolites", "Carbohydrate metabolism", 
"Energy metabolism", "Lipid metabolism", "Metabolism of cofactors and vitamins", 
"Metabolism of other amino acids", "Metabolism of terpenoids and polyketides", 
"Nucleotide metabolism", "Xenobiotics biodegradation and metabolism"
), class = "factor"), Count = c(67L, 31L, 54L, 34L, 23L, 13L, 
15L, 20L, 13L, 9L), Ratio = c(11.67, 11.07, 7.78, 8.76, 9.58, 
8.39, 7.94, 5.17, 3.27, 2.77), pval_adjusted = c(1.231153e-14, 
4.492243e-06, 2.940591e-05, 0.0002439616, 0.001488961, 0.1285896, 
0.1255625, 1, 1, 1)), .Names = c("id", "KEGG_Pathway", "Count", 
"Ratio", "pval_adjusted"), class = "data.frame", row.names = c(NA, 
-10L))

library(ggplot2)
library(RColorBrewer)
data$KEGG_Pathway <- factor(data$KEGG_Pathway, levels = rev(data$KEGG_Pathway))

myPalette <- colorRampPalette(c("red","blue","green"))(15)

ggplot(data, aes(Count, KEGG_Pathway)) + geom_point(aes(color=pval_adjusted, size=Ratio)) +
  scale_colour_gradientn(colours = myPalette, trans="log",
                         breaks = 10^(-c(0:14)), limits = c(10e-15,1)) + 
  scale_size_area(breaks = seq(0,12, by=2)) + theme_bw()