#pheatmap fraw heatmap
rm(list = ls())
library(pheatmap)
#################data
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")
dim(test) #[1] 20 10
## [1] 20 10
head(test)
## Test1 Test2 Test3 Test4 Test5 Test6 Test7
## Gene1 4.346670 0.4390334 4.2204902 -0.08586223 2.350942 1.1762784 3.116173
## Gene2 3.659478 1.8613520 2.8665830 -0.46817054 3.457590 -0.3987435 3.069913
## Gene3 3.491742 -0.7360575 2.8922225 -0.81696120 3.378185 1.4715903 4.227275
## Gene4 3.469093 -0.8283316 0.6002364 0.15905335 2.194965 -1.4236847 6.031756
## Gene5 3.567546 -0.1687894 4.1441206 1.37350655 1.308806 -0.2973308 2.122799
## Gene6 2.665930 -0.7867037 1.6955183 -1.17729223 2.053494 0.8654249 1.786659
## Test8 Test9 Test10
## Gene1 0.8506096 2.948845 0.3320269
## Gene2 -0.4212113 2.867723 0.6474985
## Gene3 -1.2093191 2.149610 -1.4299511
## Gene4 -0.9057285 2.899553 -1.1077344
## Gene5 0.7828739 2.542864 -0.5275598
## Gene6 1.3539340 2.621057 0.1497603
####################draw plot
#1.1 default parameter
pheatmap(test,scale = "row")
#clustering_method
pheatmap(test, scale = "row",
clustering_distance_rows = "correlation",
color = colorRampPalette(c("navy", "white", "firebrick3"))(50),
legend_breaks = c(-2:2), legend_labels = c("-2A","-1A","0","1B","2B"),
border_color = "red",
show_rownames=T,show_colnames=T,
treeheight_row = 50, treeheight_col = 5,
display_numbers = TRUE,number_color = "blue",number_format = "%.1e",
cellwidth = 25, cellheight = 12, main = "Example heatmap")
############1.2 annotation
###########column
annotation_col = data.frame(
CellType = factor(rep(c("CT1", "CT2"), 5)),
Time = 1:5)
rownames(annotation_col) = paste("Test", 1:10, sep = "")
annotation_col
## CellType Time
## Test1 CT1 1
## Test2 CT2 2
## Test3 CT1 3
## Test4 CT2 4
## Test5 CT1 5
## Test6 CT2 1
## Test7 CT1 2
## Test8 CT2 3
## Test9 CT1 4
## Test10 CT2 5
##########row
annotation_row = data.frame(
GeneClass = factor(rep(c("Path1", "Path2", "Path3"), c(10, 4, 6))))
rownames(annotation_row) = paste("Gene", 1:20, sep = "")
annotation_row
## GeneClass
## Gene1 Path1
## Gene2 Path1
## Gene3 Path1
## Gene4 Path1
## Gene5 Path1
## Gene6 Path1
## Gene7 Path1
## Gene8 Path1
## Gene9 Path1
## Gene10 Path1
## Gene11 Path2
## Gene12 Path2
## Gene13 Path2
## Gene14 Path2
## Gene15 Path3
## Gene16 Path3
## Gene17 Path3
## Gene18 Path3
## Gene19 Path3
## Gene20 Path3
pheatmap(test,
scale = "row",
clustering_distance_rows = "correlation",
color = colorRampPalette(c("navy", "white", "firebrick3"))(50),
legend_breaks = c(-2:2), legend_labels = c("-2A","-1A","0","1B","2B"),
border_color = "red",
show_rownames=T,show_colnames=T,
treeheight_row = 50, treeheight_col = 5,
display_numbers = TRUE,number_color = "blue",number_format = "%.1e",
cellwidth = 25, cellheight = 12, main = "Example heatmap",
annotation_row = annotation_row,
annotation_col = annotation_col, annotation_legend = T)
##########annotate color
ann_colors = list(
Time = c("white", "firebrick"),
CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E")
)
ann_colors
## $Time
## [1] "white" "firebrick"
##
## $CellType
## CT1 CT2
## "#1B9E77" "#D95F02"
##
## $GeneClass
## Path1 Path2 Path3
## "#7570B3" "#E7298A" "#66A61E"
pheatmap(test,
scale = "row",
clustering_distance_rows = "correlation",
color = colorRampPalette(c("navy", "white", "firebrick3"))(50),
legend_breaks = c(-2:2), legend_labels = c("-2A","-1A","0","1B","2B"),
border_color = "red",
show_rownames=T,show_colnames=T,
treeheight_row = 50, treeheight_col = 5,
display_numbers = TRUE,number_color = "blue",number_format = "%.1e",
cellwidth = 25, cellheight = 12, main = "Example heatmap",
annotation_col = annotation_col, annotation_legend = T,
annotation_row = annotation_row,
annotation_colors = ann_colors)
#########1.3 split col an row
pheatmap(test,
scale = "row",
clustering_distance_rows = "correlation",
color = colorRampPalette(c("navy", "white", "firebrick3"))(50),
legend_breaks = c(-2:2), legend_labels = c("-2A","-1A","0","1B","2B"),
border_color = "red",
show_rownames= T, show_colnames=T,
treeheight_row = 50, treeheight_col = 5,
display_numbers = F,number_color = "blue",number_format = "%.1e",
cellwidth = 25, cellheight = 12, main = "Example heatmap",
annotation_col = annotation_col, annotation_legend = T,
annotation_row = annotation_row,
annotation_colors = ann_colors,
cluster_rows = F,
gaps_row = c(3,9, 14), cutree_col = 2)
###########################1.4 label special rowname
labels_row = c("", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "Il10", "Il15", "Il1b")
# labels_row
pheatmap(test,
scale = "row",
clustering_distance_rows = "correlation",
color = colorRampPalette(c("navy", "white", "firebrick3"))(50),
legend_breaks = c(-2:2), legend_labels = c("-2A","-1A","0","1B","2B"),
border_color = "red",
show_rownames= T, show_colnames= T,
treeheight_row = 50, treeheight_col = 5,
display_numbers = F,number_color = "blue",number_format = "%.1e",
cellwidth = 25, cellheight = 12, main = "Example heatmap",
annotation_col = annotation_col, annotation_legend = T,
annotation_row = annotation_row,
annotation_colors = ann_colors,
cluster_rows = F,
gaps_row = c(3,9, 14), cutree_col = 2,
labels_row = labels_row)
####################1.4
aa <- pheatmap(test,scale="row")
summary(aa)
## Length Class Mode
## tree_row 7 hclust list
## tree_col 7 hclust list
## kmeans 1 -none- logical
## gtable 6 gtable list
order_row = aa$tree_row$order
order_col = aa$tree_col$order
order_row;order_col
## [1] 2 8 4 9 6 7 1 5 3 10 12 15 18 20 16 17 14 19 11 13
## [1] 5 7 9 1 3 8 2 4 6 10
#dev.off()
####################1.5FONT SIZE and saveas pdf
#pheatmap(test, cellwidth = 15, cellheight = 12, fontsize = 8, filename = "test.pdf")