rosemary94/ggheatmap

ggplot2 version of heatmap

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"))))