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Questions tagged [complexheatmap]

ComplexHeatmap is an R Bioconductor package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

The package is available on Bioconductor. Its code is on GitHub. and the documentation is here.

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Extracting row names from heatmap

I made a heatmap from my data using Complex heatmap library from R. Below is the code that I have used and also the sample data. Data Gene T1 T2 T3 T4 ARL2-SNX15 4.678845561 3.728158677 4.825892144 3.189954084 PALM 2.657130448 2.880786566…
Angelo
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ComplexHeatmap: How to place heatmap legend and annotation legend differently?

I have produced this plot with library(ComplexHeatmap) I want the Z-score at the bottom-position while the categorial variables shown on the right side. This post came close, but I cannot get it to work using rowAnnotation as in the script…
cmirian
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Adding decorate_annotation to vertical joined upset plots within ComplexHeatmap package

I am using the UpSet function from the ComplexHeatmap package and I am trying to add annotation to the graph. In the really good how-to, they describe the extra step to plot the counts next to the bars, and they also explain, why they separate this…
drmariod
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Rotate annotation in Upset plot of complex heatmap package

I want to show the numbers of the bars in the top annotation barplot in the Upset plot of ComplexHeatmap. However, I could only find parameters to rotate the name of the annotations, but not the annotations themselfes. Taken from the ComplexHeatmap…
nebroth
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R Shiny and Heatmaps - no apparent error for debugging

I am trying to create a script to generate heatmaps in R shiny. I attach the script below library(shiny) options(shiny.maxRequestSize = 50*1024^2) ui <- fluidPage( sidebarLayout( sidebarPanel( fileInput('expression_table','Expression…
geosen
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ComplexHeatmap, cannot create horizontal legend

Hi I'm using the ComplexHeatmap package and followed their vignette however for some reason I cannot seem to force the legend to become horizontal. So for example here is an example, set.seed(123) library(ComplexHeatmap) mat = matrix(rnorm(80, 2),…
Ahdee
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Cluster circular heatmap based on categorical variable

I want to plot a circular heatmap similar to the image below (obtained from here). However, I want to cluster by clin.info$subtype column, which correspond with the column names of meth and exp. library(circlize) library(ComplexHeatmap) # Split by…
melolili
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Circlize Error: Since `gap.degree` parameter has length larger than 1, it should have same length as the number of sectors

I want to plot a chord diagram using the circlize library. The gap.degree parameter is defined as the gap between two neighbour sectors. It can be a single value or a vector. If it is a vector, the first value corresponds to the gap after the first…
melolili
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superscript in row names ComplexHeatmap R

I generated a heatmap graphic with the following code: A = c(rep(100,22),rep(0,15),rep(10,12), rep(50,14)) B = c(rep(0,22),rep(8,15),rep(13,12), rep(82,14)) C = c(rep(0,22),rep(8,15),rep(13,6),rep(75,6), rep(82,14)) D =…
Juliana B C
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How to customize legends with own symbols?

recently, I am using Complexheatmap package to make heatmaps in R. After I finished making and annotating the map, I want to further include a legend about the annotation meanings. rnames <- c("+","+","+", "-", "-","δ","δ","δ","δ",…
Dr. Coke
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Barplot ComplexHeatmap

I did a barplot as column annotation on a heatmap. I use ComplexHeatmap. My input for annotation is: vector_pvalues_adj <- c(0.3778364, 0.0001000, 0.2122000, 0.4174714, 0.3778364, 0.4799250, 0.1613250, 0.4861000, 0.4174714, 0.1008000, 0.0141000,…
jonny jeep
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turn off repel in legend of complexheatmap

I would like to be able to turn off the black lines that are linked to the numbers in the legend. If I increase the width, they will disappear, but I would like to keep the width as it is. Is it possible to just add FALSE…
user2300940
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Is there any possible ways to add significant stars and brackets besides Complexheatmap

I have created the oncoprint by Complexheatmap in R like this: oncoprint I'm wondering is it possible to use ggplot or other package to add significant stars like this: significant stars besides the oncoprint? So I did column_title = "OncoPrint…
Lili
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ComplexHeatmap using column_split()

I want to plot a heatplot in r using the library(ComplexHeatmap). The reason for a complex heatmap is I want to use the function column_split() and create four sections along the x-axis of the heatmap based on the condition of the entry present in…
driver
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How to get the IDs for a specific branch from the column dendrogram in ComplexHeatmap

I have a heatmap made from over 1200 samples using ComplexHeatmap. I noticed an interesting expression pattern in the first sub-branch of the main 2 branches of the column dendrogram (circled in the image linked below). Is there any way to extract…
mfeldbauer
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