图形化数据的变化顺序

Question

我试图按照表中指定的顺序绘制我的数据，但我不知道如何绘制。我想我已经改变了水平(？)但不是因素(？)

链接到我的数据：https://docs.google.com/spreadsheets/d/1juBhHNjvsm1otxcpEFu-Zi_v5hSrNj94zdXrENOglTs/edit?usp=sharing

到目前为止，我已经：

BigTree <- read_csv(file = "/cloud/project/Phylogeny/RtreeData.csv")

Bfr <- BigTree[with(BigTree, order(-BfrA, -BfrB, -Bfd, -Ftn, -DPS, 
                                   -Rubrerythrin, -EncFtn, -NEEF)), ]
BfrLong <- pivot_longer(Bfr, 2:9) 
colnames(BfrLong) <- c("Species", "Protein", "Presence")

这可以重新排序数据，并按照我想要绘制的顺序放置数据，但是我无法绘制这个数据。错误说

错误(BfrLong，aes(x =蛋白质，y=物种，fill =存在))+：二进制运算符的非数值参数

我试着使用下面的因子函数得到相同的结果，但是它没有达到预期的效果。我在这里做错什么了？

BigTreeLong$Protein <- factor(BigTreeLong$Protein, 
                              levels = c("BfrA", "BfrB", "Bfd", "Ftn", "DPS", 
                                            "Rubrerythrin", "EncFtn", "NEEF"))

如何更改因素，以便在绘图期间维护顺序？

到目前为止，我的热图代码使用了原始的BigTree数据格式。我想排序，所以左上角开始最浅绿色，它逐渐减少到大多数深绿色的底部行。

ggplot(BigTreeLong, aes(Protein, Species, fill= Presence)) + 
  geom_tile(color = "white", linetype = 1) +
  scale_fill_gradient(low = "darkgreen", high = "olivedrab3") +
  labs(title = "Ferritins present in different bacteria", 
       x = "Ferritin family proteins", 
       y = "Species", 
       fill = "Presence of protein") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle=45, hjust=1, size=8)) +
  theme(axis.text.y = element_text(angle=0, hjust=1, size=6)) +
  scale_x_discrete(limits = c("BfrA", "BfrB", "Bfd", "Ftn", "DPS", 
                              "EncFtn", "NEEF", "Rubrerythrin"))

这是我目前制作的热图

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我希望我已经包括了我需要的一切！

Answer 1

您的物种列的级别在您的代码中没有被修改，所以您需要这一行来注册它：

BfrLong$Species=factor(BfrLong$Species,levels=Bfr$Species)

请注意示例中对象的名称，有BfrLong和BigTreeLong，但这应该有效：

BigTree <- read_csv(file = "/cloud/project/Phylogeny/RtreeData.csv")

Bfr <- BigTree[with(BigTree, order(-BfrA, -BfrB, -Bfd, -Ftn, -DPS, 
                                   -Rubrerythrin, -EncFtn, -NEEF)), ]
BfrLong <- pivot_longer(Bfr, 2:9) 
colnames(BfrLong) <- c("Species", "Protein", "Presence")

BfrLong$Species=factor(BfrLong$Species,levels=Bfr$Species)

ggplot(BfrLong, aes(Protein, Species, fill= Presence)) + 
  geom_tile(color = "white", linetype = 1) +
  scale_fill_gradient(low = "darkgreen", high = "olivedrab3") +
  labs(title = "Ferritins present in different bacteria", 
       x = "Ferritin family proteins", 
       y = "Species", 
       fill = "Presence of protein") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle=45, hjust=1, size=8)) +
  theme(axis.text.y = element_text(angle=0, hjust=1, size=6)) +
  scale_x_discrete(limits = c("BfrA", "BfrB", "Bfd", "Ftn", "DPS", 
                              "EncFtn", "NEEF", "Rubrerythrin"))

​

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