ggheatmap
ggplot2 Version of Heatmap
Install Package
- Method1.Download from Github
devtools::install_github("XiaoLuo-boy/ggheatmap") - Method2.Download from CRAN
install.packages("ggheatmap")
function list
- ggheatmap() Draw a heatmap
- ggheatmap_theme() Set the styles of the drawing elements of each component of the ggheatmap except cluster tree
- ggheatmap_plotlist() Display the basic elements of the ggheatmap
ggheatmap() Parameter Description
- data input data(matrix or data.frame)
- color the color of heatmap
- legendName character,the title of heatmap legend
- scale character,the way of scale data("none", "row" or "column")
- border character, the colour of border
- shape character, the shape of cell("square", "circle" and "triangle").Default is NULL
- cluster_rows whether rows should be clustered(TRUE of FALSE)
- cluster_cols whether column should be clustered(TRUE of FALSE)
- dist_method character,the method parameter of dist function. see dist
- hclust_method character,the method parameter of hclust function, see hclust
- text_show_rows a character you want to show for y-axis
- text_show_cols a character you want to show for x-axis
- text_position_rows character,the position of y-axis label("right" or "left")
- text_position_cols character,the position of x-axis label("bottom" or "top")
- annotation_cols a data.frame for column annotation
- annotation_rows a data.frame for row annotation
- annotation_color a list for annotation color
- annotation_width a numeric for annotation width
- annotation_position_rows character,the position of column annotation("right" or "left")
- annotation_position_cols character,the position of row annotation("bottom" or "top")
- show_cluster_cols whether show column cluster tree(TRUE of FALSE)
- show_cluster_rows whether show row cluster tree(TRUE of FALSE)
- cluster_num a numeric for cut cluster tree
- tree_height_rows row cluster tree height
- tree_height_cols column cluster tree height
- tree_color_rows a character for row cluster tree color
- tree_color_cols a character for column cluster tree color
- tree_position_rows character,the position of row cluster tree("right" or "left")
- tree_position_cols character,the position of column cluster tree("bottom" or "top")
- levels_rows a character for y-axis label levels
- levels_cols a character for x-axis label levels
Usage
devtools::install_github("XiaoLuo-boy/ggheatmap")
install.packages("ggheatmap")
library(ggheatmap)
library(tidyr)
set.seed(123)
df <- matrix(runif(225,0,10),ncol = 15)
colnames(df) <- paste("sample",1:15,sep = "")
rownames(df) <- sapply(1:15, function(x)paste(sample(LETTERS,3,replace = F),collapse = ""))
df[1:4,1:4]
row_metaData <- data.frame(exprtype=sample(c("Up","Down"),15,replace = T),
genetype=sample(c("Metabolism","Immune","None"),15,replace = T))
rownames(row_metaData) <- rownames(df)
col_metaData <- data.frame(tissue=sample(c("Normal","Tumor"),15,replace = T),
risklevel=sample(c("High","Low"),15,replace = T))
rownames(col_metaData) <- colnames(df)
exprcol <- c("#EE0000FF","#008B45FF" )
names(exprcol) <- c("Up","Down")
genecol <- c("#EE7E30","#5D9AD3","#D0DFE6FF")
names(genecol) <- c("Metabolism","Immune","None")
tissuecol <- c("#98D352","#FF7F0E")
names(tissuecol) <- c("Normal","Tumor")
riskcol <- c("#EEA236FF","#46B8DAFF")
names(riskcol) <- c("High","Low")
col <- list(exprtype=exprcol,genetype=genecol,tissue=tissuecol,risklevel=riskcol)
text_rows <- sample(rownames(df),3)
p<- ggheatmap(df,cluster_rows = T,cluster_cols = T,scale = "row",
text_show_rows = text_rows,
cluster_num = c(3,3),
tree_color_rows = c("#008B45FF","#631879FF","#008280FF"),
tree_color_cols = c("#1F77B4FF","#FF7F0EFF","#2CA02CFF"),
annotation_rows = row_metaData,
annotation_cols = col_metaData,
annotation_color = col
)
p
Show your basic elements of the ggheatmap
ggheatmap_plotlist(p)
Use ggheatmap_theme to make your figure more elegant
p%>%
ggheatmap_theme(1:5,
theme =list(
theme(axis.text.x = element_text(angle = 90,face = "bold",size = 10),
axis.text.y = element_text(colour = "red",face = "bold")),
theme(legend.title = element_text(face = "bold")),
theme(legend.title = element_text(face = "bold")),
theme(legend.title = element_text(face = "bold")),
theme(legend.title = element_text(face = "bold"))
))
Set your border color
ggheatmap(df,cluster_rows = T,cluster_cols = T,scale = "row",
text_show_rows = text_rows,
border = "grey",
cluster_num = c(3,3),
tree_color_rows = c("#008B45FF","#631879FF","#008280FF"),
tree_color_cols = c("#1F77B4FF","#FF7F0EFF","#2CA02CFF"),
annotation_rows = row_metaData,
annotation_cols = col_metaData,
annotation_color = col
)%>%
ggheatmap_theme(1,theme =list(theme(axis.text.x = element_text(angle = 90,face = "bold",size = 10),
axis.text.y = element_text(colour = "red",face = "bold"))))
Chage your heatmap cell shape
ggheatmap(df,cluster_rows = T,cluster_cols = T,scale = "row",
text_show_rows = text_rows,
border = "grey",
shape = "circle",
cluster_num = c(3,3),
tree_color_rows = c("#008B45FF","#631879FF","#008280FF"),
tree_color_cols = c("#1F77B4FF","#FF7F0EFF","#2CA02CFF"),
annotation_rows = row_metaData,
annotation_cols = col_metaData,
annotation_color = col
)%>%
ggheatmap_theme(1,theme =list(theme(axis.text.x = element_text(angle = 90,face = "bold",size = 10),
axis.text.y = element_text(colour = "red",face = "bold"))))
Position
ggheatmap(df,cluster_rows = T,cluster_cols = T,scale = "row",
text_show_rows = text_rows,
border = "grey",
cluster_num = c(3,3),
tree_color_rows = c("#008B45FF","#631879FF","#008280FF"),
tree_color_cols = c("#1F77B4FF","#FF7F0EFF","#2CA02CFF"),
annotation_rows = row_metaData,
annotation_cols = col_metaData,
annotation_color = col,
text_position_rows = "left",
text_position_cols = "top",
tree_position_rows = "right",
tree_position_cols = "bottom",
annotation_position_rows = "right",
annotation_position_cols = "bottom"
)%>%
ggheatmap_theme(1,theme =list(theme(axis.text.x = element_text(angle = 90,face = "bold",size = 10),
axis.text.y = element_text(colour = "red",face = "bold"))))