### Install and Initialize ggheatmap

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/README.md

Install the package from GitHub or CRAN and prepare the sample data matrix and metadata.

```R
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
```

--------------------------------

### Install ggheatmap from CRAN

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/README.md

Use the standard R package installation command to install from CRAN.

```R
install.packages("ggheatmap")
```

--------------------------------

### Install ggheatmap from GitHub

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/README.md

Use devtools to install the package directly from the GitHub repository.

```R
devtools::install_github("XiaoLuo-boy/ggheatmap")
```

--------------------------------

### Create and Customize a Heatmap

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap.Rd

Demonstrates generating a heatmap with row scaling and clustering, followed by theme customization using aplot.

```R
#Create data
library(ggheatmap)
library(tidyr)
library(aplot)
set.seed(123)
df <- matrix(runif(600,0,10),ncol = 12)
colnames(df) <- paste("sample",1:12,sep = "")
rownames(df) <- sapply(1:50, function(x)paste(sample(LETTERS,3,replace = FALSE),collapse = ""))
head(df)
#example 1
text_rows <- sample(rownames(df),3)
p <- ggheatmap(df,scale = "row",cluster_rows  = TRUE,cluster_cols = TRUE,
          text_show_rows = text_rows)\%>\%
          ggheatmap_theme(1,theme =list(
           theme(axis.text.x = element_text(angle = 90,face = "bold"),
           axis.text.y = element_text(colour = "red",face = "bold"))
  ))
```

--------------------------------

### Generate Heatmap with Clustering and Shapes

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap.Rd

Shows how to create a heatmap with specific cell shapes, cluster counts, and custom tree colors.

```R
#example 2
ggheatmap(df,cluster_rows = TRUE,cluster_cols = TRUE,
          border = "grey",
          shape = "circle",
          cluster_num = c(5,4),
          tree_color_rows = c("#3B4992FF","#EE0000FF","#008B45FF","#631879FF","#008280FF"),
          tree_color_cols = c("#0073C2FF", "#EFC000FF" ,"#868686FF", "#CD534CFF")
)
```

--------------------------------

### Generate and style a heatmap with ggheatmap

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/README.md

Configures heatmap clustering, annotations, and positions, then applies a custom theme using ggheatmap_theme.

```R
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"))))
```

--------------------------------

### Create a complex heatmap with annotations and themes

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap.Rd

Generates a heatmap with row and column metadata, clustering, and custom color schemes, followed by theme adjustments.

```R
row_metaData <- data.frame(exprtype=sample(c("Up","Down"),50,replace = TRUE),
genetype=sample(c("Metabolism","Immune","None"),50,replace = TRUE))
rownames(row_metaData) <- rownames(df)
col_metaData <- data.frame(tissue=sample(c("Normal","Tumor"),12,replace = TRUE),
                           risklevel=sample(c("High","Low"),12,replace = TRUE))
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)

p<- ggheatmap(df,cluster_rows = TRUE,cluster_cols = TRUE,scale = "row",
              cluster_num = c(5,3),
              tree_color_rows = c("#3B4992FF","#EE0000FF","#008B45FF","#631879FF","#008280FF"),
              tree_color_cols = c("#1F77B4FF","#FF7F0EFF","#2CA02CFF"),
              annotation_rows = row_metaData,
              annotation_cols = col_metaData,
              annotation_color = col
)
p
ggheatmap_theme(p,2:5,theme = list(
  theme(legend.text = element_text(face = "bold")),
  theme(legend.text = element_text(face = "bold")),
  theme(legend.text = element_text(face = "bold")),
  theme(legend.text = element_text(face = "bold"))

))
```

--------------------------------

### ggheatmap_plotlist(ggheatmap)

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap_plotlist.Rd

Displays the basic elements of a ggheatmap object.

```APIDOC
## ggheatmap_plotlist

### Description
Display the basic elements of the ggheatmap.

### Usage
`ggheatmap_plotlist(ggheatmap)`

### Arguments
- **ggheatmap** (heatmap) - The result object of a ggheatmap call.

### Returns
- **plotlist** - A list of plots contained within the ggheatmap object.
```

--------------------------------

### ggheatmap_theme(ggheatmap, plotlist, theme)

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap_theme.Rd

Sets the styles of the drawing elements for specific components within a ggheatmap object.

```APIDOC
## ggheatmap_theme

### Description
Set the styles of the drawing elements of each component of the ggheatmap except cluster tree.

### Usage
ggheatmap_theme(ggheatmap, plotlist, theme)

### Arguments
- **ggheatmap** (object) - The result of a ggheatmap call.
- **plotlist** (integer) - The plotlist index in ggheatmap. Use ggheatmap_plotlist for reference.
- **theme** (list) - The theme settings for the plotlist. See the standard theme documentation for more details.

### Returns
- **ggheatmap** (object) - The modified ggheatmap object.
```

--------------------------------

### ggheatmap(df, ...)

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap.Rd

Generates a heatmap from a data frame with options for clustering, scaling, and adding annotations.

```APIDOC
## ggheatmap(df, ...)

### Description
Creates a heatmap visualization from a provided data frame. Supports row and column clustering, data scaling, and integration with metadata annotations.

### Parameters
- **df** (data.frame) - The input data frame to visualize.
- **cluster_rows** (boolean) - Whether to perform hierarchical clustering on rows.
- **cluster_cols** (boolean) - Whether to perform hierarchical clustering on columns.
- **scale** (string) - Scaling method for the data (e.g., "row").
- **cluster_num** (vector) - Number of clusters for rows and columns.
- **tree_color_rows** (vector) - Colors for row dendrogram branches.
- **tree_color_cols** (vector) - Colors for column dendrogram branches.
- **annotation_rows** (data.frame) - Metadata for row annotations.
- **annotation_cols** (data.frame) - Metadata for column annotations.
- **annotation_color** (list) - Color mapping for annotations.
- **annotation_position_rows** (string) - Position of row annotations (e.g., "right").
```

--------------------------------

### ggheatmap(data, ...)

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap.Rd

Generates a heatmap visualization based on the provided matrix or data frame, with options for clustering, scaling, and annotation.

```APIDOC
## Function: ggheatmap

### Description
Creates a heatmap using the ggplot2 system. It allows for flexible label settings, clustering tree visualization, and integration with other ggplot2 objects.

### Parameters
- **data** (matrix/data.frame) - Required - Input data for the heatmap.
- **color** (vector) - Optional - Color palette for the heatmap.
- **legendName** (character) - Optional - Title of the heatmap legend.
- **scale** (character) - Optional - Scaling method: "none", "row", or "column".
- **shape** (character) - Optional - Cell shape: "square", "circle", or "triangle".
- **cluster_rows** (boolean) - Optional - Whether to cluster rows.
- **cluster_cols** (boolean) - Optional - Whether to cluster columns.
- **dist_method** (character) - Optional - Distance method for clustering (see dist).
- **hclust_method** (character) - Optional - Clustering method (see hclust).
- **annotation_cols** (data.frame) - Optional - Column annotations.
- **annotation_rows** (data.frame) - Optional - Row annotations.
- **annotation_color** (list) - Optional - Colors for annotations.

### Returns
- **p** (ggplot object) - The resulting heatmap object.
```

--------------------------------

### Customize heatmap annotation position

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap.Rd

Demonstrates how to specify the position of row annotations in the heatmap.

```R
ggheatmap(df,cluster_rows = TRUE,cluster_cols = TRUE,scale = "row",
          cluster_num = c(5,3),
          tree_color_rows = c("#3B4992FF","#EE0000FF","#008B45FF","#631879FF","#008280FF"),
          tree_color_cols = c("#1F77B4FF","#FF7F0EFF","#2CA02CFF"),
          annotation_rows = row_metaData,
          annotation_cols = col_metaData,
          annotation_color = col,
          annotation_position_rows="right"
)
```

--------------------------------

### ggheatmap()

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/README.md

The primary function to draw a heatmap with various customization options for data scaling, clustering, and annotations.

```APIDOC
## ggheatmap(data, ...)

### Description
Draws a heatmap based on the provided input data.

### Parameters
- **data** (matrix or data.frame) - Required - Input data
- **color** (character) - Optional - The color of the heatmap
- **legendName** (character) - Optional - The title of the heatmap legend
- **scale** (character) - Optional - The way of scale data ("none", "row" or "column")
- **border** (character) - Optional - The colour of the border
- **shape** (character) - Optional - The shape of cell ("square", "circle" and "triangle")
- **cluster_rows** (boolean) - Optional - Whether rows should be clustered
- **cluster_cols** (boolean) - Optional - Whether column should be clustered
- **dist_method** (character) - Optional - The method parameter of dist function
- **hclust_method** (character) - Optional - The method parameter of hclust function
- **text_show_rows** (character) - Optional - Labels to show for y-axis
- **text_show_cols** (character) - Optional - Labels to show for x-axis
- **text_position_rows** (character) - Optional - Position of y-axis label ("right" or "left")
- **text_position_cols** (character) - Optional - Position of x-axis label ("bottom" or "top")
- **annotation_cols** (data.frame) - Optional - Data for column annotation
- **annotation_rows** (data.frame) - Optional - Data for row annotation
- **annotation_color** (list) - Optional - Colors for annotation
- **annotation_width** (numeric) - Optional - Width for annotation
- **annotation_position_rows** (character) - Optional - Position of column annotation ("right" or "left")
- **annotation_position_cols** (character) - Optional - Position of row annotation ("bottom" or "top")
- **show_cluster_cols** (boolean) - Optional - Whether to show column cluster tree
- **show_cluster_rows** (boolean) - Optional - Whether to show row cluster tree
- **cluster_num** (numeric) - Optional - Number for cutting cluster tree
- **tree_height_rows** (numeric) - Optional - Row cluster tree height
- **tree_height_cols** (numeric) - Optional - Column cluster tree height
- **tree_color_rows** (character) - Optional - Color for row cluster tree
- **tree_color_cols** (character) - Optional - Color for column cluster tree
- **tree_position_rows** (character) - Optional - Position of row cluster tree ("right" or "left")
- **tree_position_cols** (character) - Optional - Position of column cluster tree ("bottom" or "top")
- **levels_rows** (character) - Optional - Levels for y-axis label
- **levels_cols** (character) - Optional - Levels for x-axis label
```

--------------------------------

### Display Heatmap Elements

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/README.md

Extract and display the individual components of the generated heatmap object.

```R
ggheatmap_plotlist(p)
```

--------------------------------

### Append ggplot2 objects to heatmap

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap.Rd

Shows how to insert an additional ggplot2 visualization to the side of the heatmap.

```R
dat <- data.frame(marker=sample(c(1,NA),50,replace = TRUE),
gene=rownames(df),
shape=sample(c("T","F"),50,replace = TRUE))
p1 <- ggplot(dat,aes(x=1,y=gene,size=marker,color=shape,shape=shape))+
  geom_point()+theme_classic()+
  scale_color_manual(values = c("#D2691E","#1E87D2"))+
  theme(line = element_blank(),axis.text = element_blank(),axis.title = element_blank())+
  guides(size = FALSE)

p%>%insert_right(p1,width = 0.1)
```

--------------------------------

### ggheatmap_theme(p, indices, theme)

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/man/ggheatmap.Rd

Applies custom ggplot2 themes to specific components of a ggheatmap object.

```APIDOC
## ggheatmap_theme(p, indices, theme)

### Description
Modifies the theme of specific elements within a generated ggheatmap object.

### Parameters
- **p** (object) - The ggheatmap object.
- **indices** (vector) - Numeric indices of the heatmap components to modify.
- **theme** (list) - A list of ggplot2 theme objects to apply.
```

--------------------------------

### Customize Heatmap Theme

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/README.md

Apply ggplot2 themes to specific elements of the heatmap using the pipe operator.

```R
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 Heatmap Border Color

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/README.md

Define the border color for heatmap cells during the initial function call.

```R
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"))))
```

--------------------------------

### Change Heatmap Cell Shape

Source: https://github.com/xiaoluo-boy/ggheatmap/blob/main/README.md

Modify the visual representation of heatmap cells by setting the shape parameter to 'circle'.

```R
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"))))
```

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