R
R | Clustering된 Heatmap 그리기, pheatmap,
Chloe A_Choe
2020. 1. 16. 14:06
pheatmap을 이용해서 clustering된 heatmap을 그리는 방법
(본 포스팅에 사용된 데이터 셋은 위 링크를 통해 받을 수 있습니다.)
# 목표 히트맵
1. Importing Test Data
> myData <- read.csv(sprintf('C:/chloe-with-data/Heatmap_Cluster/matrix.csv'), header = T, row.names = 1)
> myData %>% dim
[1] 15 15
> myData %>% head
A B C D E F G H I J K L M N O
A 100.0 79.7 79.8 80.6 80.4 80.9 80.0 79.9 79.1 94.6 79.7 94.7 95.0 95.0 78.8
B 79.7 100.0 84.8 84.7 84.3 86.0 92.0 85.3 83.6 80.3 85.0 79.8 79.8 78.7 85.3
C 79.8 84.8 100.0 88.9 90.7 90.9 84.7 88.8 85.6 79.8 93.4 79.6 79.6 79.9 85.6
D 80.6 84.7 88.9 100.0 89.6 89.7 84.8 88.3 85.0 80.8 88.8 80.6 80.7 80.6 85.6
E 80.4 84.3 90.7 89.6 100.0 94.6 84.7 89.4 85.0 80.3 89.8 80.4 80.4 79.5 86.8
F 80.9 86.0 90.9 89.7 94.6 100.0 85.9 89.7 86.7 80.9 90.1 80.6 80.6 80.8 87.3
2. pheatmap : default
> p <- pheatmap(myData)
> p
3. pheatmap : without clustering
> p <- pheatmap(myData,
+ cluster_rows = F,
+ cluster_cols = F)
> p
3. pheatmap : with values
> p <- pheatmap(myData,
+ display_numbers = T)
> p
4. pheatmap : white border
> p <- pheatmap(myData,
+ display_numbers = T,
+ border_color = 'white')
> p
5. pheatmap : show colnames False
> p <- pheatmap(myData,
+ display_numbers = T,
+ border_color = 'white',
+ show_colnames = F,
+ show_rownames = T)
>
6. pheatmap : cutree
> p <- pheatmap(myData,
+ display_numbers = T,
+ border_color = 'white',
+ show_colnames = F,
+ show_rownames = T,
+ cutree_rows = 2,
+ cutree_cols = 2)
> p
3. pheatmap : set color
> p <- pheatmap(myData,
+ cutree_rows = 2,
+ cutree_cols = 2,
+ color = colorRampPalette(c('#2471A3','white','#C0392B'))(50),
+ border_color = 'white',
+ display_numbers = T,
+ show_colnames = F,
+ show_rownames = T)
> p
