Questions tagged [heatmap]

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"Error in col2rgb(colors, alpha = TRUE) : invalid RGB specification" when running HeatmapAnnotation() (from ComplexHeatmap)

This question was also asked on github I'm trying to run the function HeatmapAnnotation (a function in the ComplexHeatmap package). When I run it, I get the error "Error in col2rgb(colors, alpha =...
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0 answers
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Heat map of protein expression from normalized abundance

This is a follow up to my question posted here Processing proteomics data In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article ...
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1 answer
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Constructing Two Triangle Heatmaps in One Square

I'm looking to make a two, two range colour scheme heatmap where each range corresponds to a separate triangle in the heatmap square. I am looking for a relevant guide for this heatmap. Any ...
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-1 votes
1 answer
51 views

Selecting a part of heatmap

I have a heatmap I see a block of genes for a group of samples How I can select a part of heatmap? I mean is there any way to export a list of genes from rows of a heatmap in R? I have tried which ...
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2 votes
1 answer
161 views

In a RNA-Seq heatmap should you do Z-score standardisation before clustering the rows/columns or after?

I have made a heatmap using RPKM values from a RNA-Seq dataset using the pheatmap() function in R. I have log2-transformed the data before performing Z-score standardisation of the data. I have also ...
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1 vote
1 answer
102 views

RNA-Seq Data Heatmap: Is it necessary to do a log2 transformation of RPKM values before doing the Z-score standardisation?

I am making a heatmap using RNA-Seq data in R. The heatmap shows gene expression values (RPKM) in different brain regions. I have the following code: ...
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  • 157
1 vote
1 answer
93 views

Best methods for clustering heatmap based on regions where the genes are most highly expressed?

I am analysing RNA-Seq data for a set of genes from different human brain regions using data from the Allen Brain Atlas. I have made a heatmap using GraphPad Prism. In this heatmap, I show the average ...
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  • 157
1 vote
1 answer
341 views

Changing the order of colors in pheatmap

I plotted a heatmap I want cancer to be red and healthy to be blue ...
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1 vote
0 answers
16 views

General Question: Statistical Alternatives to Oncoprint

I am a computational genomics student who has recently joined a research lab as an RA. We often work with oncoprints (comuts/heatmaps), and we visualize molecular signatures by reorganizing the comut. ...
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0 votes
1 answer
335 views

Avoiding the warning 'The following features were omitted as they were not found in the scale.data slot for the SCT assay' in Seurat

I have a Seurat object I want to plot a list of genes but I got a warning saying most of genes removed I have tried with both my genes of interest and all variable genes but the results is very ...
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-1 votes
1 answer
249 views

Seurat heatmap for two conditions

I have a Seurat object of four cancers and four controls ...
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-1 votes
1 answer
1k views

Visualizing FindMarkers result in Seurat using Heatmap

I used FindMarkers to find the DEGs between two clusters in my dataset using Seurat. I am trying to visualize the outcome using a heatmap but I failed to write the command in R. ...
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1 answer
189 views

I want to display color key on my heatmap

...
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3 votes
1 answer
973 views

Removing Batch Effect in Heatmaps after Differential Gene Expression Analysis

I'm working on a dataset in which the first replicate of each group is one batch and the second replicate is in a second batch. After checking the PCA plot and ...
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0 votes
1 answer
134 views

Adding legend to Botton and top annotation in complexheatmap

I have a heat map but top and bottom annotation don't have legend ...
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0 votes
1 answer
54 views

Is there a way to customize what observations are plotted in ComplexHeatmap?

So right now my observations in the dataset I've processed is stored as sample identifier columns and gene rows: an example of this would be for sample 1 and gene TRIM21 the observation is Missense ...
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1 vote
3 answers
2k views

Is there an "official" standard usage of Red and Green on differential gene expression heatmaps?

I have recently found myself making multiple heatmaps for visualization of differential gene expression results between replicates in two experimental conditions. The default settings in the plotting ...
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2 votes
1 answer
1k views

How can I plot multiple sequence alignment in R as a heatmap

I have many amino acids sequences in a fasta format that I did multiple sequence alignment. I was trying to plot something like binary a code as heatmap. If it had a change in the AA compared to the ...
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-3 votes
1 answer
123 views

Is it possible to get such a plot [closed]

I wish to reproduce a very informative plot in google Given a group of samples and a list of genes for which we have data how each genes has mutated and whether the alleles are homozygous of ...
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-5 votes
1 answer
63 views

How to visualise the proportion of clonal genes to sub clonal genes [duplicate]

I have a data frame ...
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  • 1,521
1 vote
1 answer
241 views

Heatmap annotation with value and colour gradient

I am trying to use ComplexHeatmap to plot heatmap with annotation. The code that I have tried ...
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0 votes
0 answers
224 views

Create a Heatmap that uses modules of genes rather than individual genes in Seurat

Is it possible to create a Heatmap in Seurat that takes in and displays modules of genes as its features rather than individual genes? So if I have a module of genes associated with a trait or ...
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0 answers
2k views

Create heat map that groups genes by expression within cluster in Seurat

I have a set of cells that I am performing Drop-seq on to look at cell expression. Among my heat maps for gene expression I want to be able to graph them similar to the graph below: Where the cells ...
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1 vote
0 answers
106 views

Argument stopped working

I am using ComplexHeatmap package for transcriptomic analyses and all of a sudden, row_labels and column_labels as well as <...
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1 vote
2 answers
249 views

How to transform and sort the matrix to make a heatmap showing signatures?

I have a matrix data with cells as rows and samples as columns. Here I am giving the data with dput ...
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1 vote
1 answer
4k views

DoHeatmap Hierarchical Clustering Seurat

I have a list of genes that I'd like to visualize using the DoHeatmap function in Seurat. However, the output of the heatmap does not result in hierarchical clustering and therefore makes it very ...
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-1 votes
1 answer
65 views

How I normalize these two sets of data

I have average log fold change for a cluster of cells versus another cluster of cells by Seurat like below ...
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1 vote
1 answer
579 views

Align legends to each heatmap in a ComplexHeatmap with 2 heatmaps

I have created a ComplexHeatmap containing 2 Heatmaps, each with their own legend. The legend on the first Heatmap is continuous, whereas that of the second is ...
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2 votes
2 answers
3k views

How do I add a colour annotation bar to the heatmap generated by DoHeatmap function of Seurat v2?

I am using Seurat v2 for professional reasons (I am aware of the availablity of Seurat v3). I am clustering and analysing single cell RNA seq data. How do I add a coloured annotation bar to the ...
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  • 487
2 votes
1 answer
1k views

Complexheatmap update issue

After i updated my complexheatmap library i can;t use my old annotation to label sample this is the image how i used to get something like this Code for the below image ...
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  • 1,538
2 votes
0 answers
992 views

GO Term heatmap plot in terms of P value or fold enrichment

I'm clustering genes in terms of expression after clustering them. I'm taking out clusters and trying to find out what kind of GO terms are coming up. I came across this figure from this paper, I want ...
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  • 1,538
2 votes
1 answer
2k views

How I can reproduce this heat map

I have single cell RNA-seq on 8 time points. I have clustered each time point to 2-3 clusters by seurat. I also have a list of differentially expressed genes between all my 1562 cells in 8 time points....
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  • 1,521
6 votes
3 answers
5k views

plotting two heatmaps with the same order of genes

I expected the same pattern but here I am not able to compare the patterns as the order of genes does not seem the same. I mean how I can have two heat maps on which the order of genes are the same so ...
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  • 1,521
2 votes
0 answers
80 views

how to plot LD between SNPs and CNVs

I have a bunch of CNVs which I have estimated LD between each allele of CNV with all SNPs across the entire human genome. I used my R-script to do a pairwise LD analysis. The following is the first ...
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