How do I use the pheatmap function?
The pheatmap function is similar to the default base R heatmap, but provides more control over the resulting plot. You can pass a numeric matrix containing the values to be plotted. If the values of the matrix are not normalized you can normalize them by rows ( "row") or by columns ( "column") making use of the scale argument.
What is the pheatmap package?
The pheatmap package, created by Raivo Kolde, offers extensive control over dimensions and appearance of heatmaps. A big advantage of the package is that it enables the user to visually cluster heatmaps. Before we dive deeper into the exemplifying R codes… Here you can find the documentation of the pheatmap package.
How are the default color breaks in pheatmap distributed?
The default color breaks in pheatmap are uniformly distributed across the range of the data. We can see that values in group 1 are larger than values in groups 2 and 3. However, we can't distinguish different values within groups 2 and 3.
How do I make a heatmap with pheatmap R?
Here are a few tips for making heatmaps with the pheatmap R package by Raivo Kolde. We'll use quantile color breaks, so each color represents an equal proportion of the data. We'll also cluster the data with neatly sorted dendrograms, so it's easy to see which samples are closely or distantly related.
How do you read Pheatmap?
0:294:50pheatmap R Tutorial - YouTubeYouTubeStart of suggested clipEnd of suggested clipThey come in handy when you have two categorical variables and a quantitative variable. TheMoreThey come in handy when you have two categorical variables and a quantitative variable. The quantitative values are represented by a colored box with two categorical variables intersect.
What is a Pheatmap?
pheatmap A function to draw clustered heatmaps. Description. A function to draw clustered heatmaps where one has better control over some graphical parameters such as cell size, etc. Usage. pheatmap(mat, color = colorRampPalette(rev(brewer.
How do I stop Pheatmap clustering?
If you want to turn off the clustering, you can set either cluster_cols or cluster_rows to False.
How do you remove a Dendrogram from Pheatmap?
How to remove dendrogram from pheatmaps? To hide the dendrogram in pheatmap you can set the argument treeheight_row or treeheight_col to zero. Do note that pheatmap is a CRAN package, so you should probably be asking your question on [email protected], or perhaps stackoverflow.com.
What clustering does Pheatmap use?
kmeans clusteringThe function also allows to aggregate the rows using kmeans clustering. This is advisable if number of rows is so big that R cannot handle their hierarchical clustering anymore, roughly more than 1000.
How do you use a heatmap?
Click maps show you an aggregate of where visitors click their mouse on desktop devices and tap their finger on mobile devices (in this case, they are known as touch heatmaps). The map is color-coded to show the elements that have been clicked and tapped the most (red, orange, yellow).
How do you split a heatmap?
You can split the heatmap by the subgroup variable (see Section 2.7), or you can use cluster_within_group() clustering function to generate a special dendrogram.
How do you save ComplexHeatmap?
According to ComplexHeatmap guide (https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html) you just need to save you heatmap as a new variable and then use draw() function to create plot in the pdf file.
What does a Dendrogram show?
A dendrogram is a branching diagram that represents the relationships of similarity among a group of entities. Each branch is called a clade.
What is Cutree function in R?
Remember from the video that cutree() is the R function that cuts a hierarchical model. The h and k arguments to cutree() allow you to cut the tree based on a certain height h or a certain number of clusters k.
The pheatmap function
The pheatmap function is similar to the default base R heatmap, but provides more control over the resulting plot. You can pass a numeric matrix containing the values to be plotted.
Clustering
You can pass a hclust object to the cluster_rows argument or set it to FALSE to remove the rows dendrogram.
Color customization
The border_color controls the border of the cells. The default value is "grey60".
Legend customization
The breaks of the legend can be customized with legend_breaks, passing the desired values as a vector.
Description
A function to draw clustered heatmaps where one has better control over some graphical parameters such as cell size, etc.
Details
The function also allows to aggregate the rows using kmeans clustering. This is advisable if number of rows is so big that R cannot handle their hierarchical clustering anymore, roughly more than 1000. Instead of showing all the rows separately one can cluster the rows in advance and show only the cluster centers.
Saving heatmap
To output the heatmap as a PNG file, save the heatmap as an object and use the grid.draw () function on the gtable slot.
Summary
There are various heatmap packages in R. I like pheatmap mainly because of its annotation feature; other heatmap packages may be able to do the same thing but I’m happy with pheatmap. Use ?pheatmap to find out more ways you can customise your heatmap.
Basic Information about the pheatmap Package
The pheatmap package, created by Raivo Kolde, offers extensive control over dimensions and appearance of heatmaps. A big advantage of the package is that it enables the user to visually cluster heatmaps.
Example 1: Draw Default Heatmap Using pheatmap Package
The following code shows how to draw a heatmap using the pheatmap function. Note that we do not have to specify anything, but the name of our data matrix that we want to draw.
Example 2: Draw Heatmap with kmeans Clusters
The pheatmap function provides numerous optional parameters that can be used to make the heatmap prettier, and to show additional clusters in the heatmap.
Example 3: Draw Heatmap with Row Clusters
In Example 3, I’ll show how to split our heatmap without combining the cells in the different clusters (as in Example 2).
Example 4: Draw Heatmap with Row & Column Clusters
This example demonstrates how to split a heatmap by rows and columns (not only by rows as in Example 3).
Video & Further Resources
I have recently published a video on my YouTube channel, which illustrates the R programming codes of this article. You can find the video below.