Question

我正在尝试使用ggplot2创建一个图，但颜色条不代表实际数据。情节看起来不错。

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

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()

情节看起来与我想要的完全一样。但是颜色条是完全疯狂的（我想要一个渐变条显示我的矢量值中的限制，以及调色板中的所有颜色，如here中所示）：

我玩过导演=＆＃34; colorbar＆＃34;和guide_colorbar（）但它始终产生这一点。

Answer 1

具有对数刻度的色彩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()

颜色不均匀，R ggplot2 scale_color_gradient

1 个答案: