如何从TCGA制作热图？

Question

我在处理TCGA数据时遇到了很多麻烦，如何制作一个热图？

a <- c(1,2,2)
b <- c(333,73,382)
c <- c(881,5,5)
wd<- data_frame(a,b,c)
colnames(wd) <- c("TCGA-55-8615-01A","TCGA-97-8177-01A","TCGA-86-8674-01A")
rownames(wd) <- c("UPK3B","GPM6A","LGI3")
wd 

示例:数据:wd

Answer 1

最简单的方法是使用heatmap来完成它。这要求您的数据是一个数字矩阵，因此您可以：

heatmap(as.matrix(t(wd)))

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如果希望完全控制外观和主题元素，可以使用ggplot

library(tidyverse)

wd %>% 
  rownames_to_column() %>%
  pivot_longer(-1, names_to = "TCGA") %>%
  ggplot(aes(rowname, TCGA, fill = value)) +
  geom_tile(color = "white") +
  scale_fill_viridis_c(option = 10) +
  theme_minimal(base_size = 16) +
  labs(x = NULL, y = NULL)

​

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可复制数据取自问题

wd <- data.frame("TCGA-55-8615-01A" = c(1, 2, 2),
           "TCGA-97-8177-01A" = c(333, 73, 382),
           "TCGA-86-8674-01A" = c(881, 5, 5),
           row.names =  c("UPK3B", "GPM6A", "LGI3"),
           check.names = FALSE)