Questions tagged [heatmap]

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Ordering average of gene expression in heat map

I want to plot a heat map in header I have the average of gene expression validated in lab for each sample ...
Zizogolu's user avatar
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3 votes
1 answer
174 views

heatmap of specific sequence motifs in aligned fasta files

I have a collection of fasta files, each containing three aligned sequences. I am interested in understanding the distribution of a specific sequence motif PGP, RGP and KGP in all the alignments. I ...
Jalan's user avatar
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1 answer
106 views

Heatmap of motifs present in protein sequences

I have a file containing multiple protein amino acid sequences. I am interested in visually presenting the location of amino acid motifs PQG, QQG and AQG in the sequence in the form of a heatmap in R. ...
Jalan's user avatar
  • 31
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2 answers
688 views

"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 =...
Lou_A's user avatar
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2 votes
1 answer
1k views

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 ...
Natasha's user avatar
  • 125
3 votes
1 answer
428 views

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 ...
raysteven's user avatar
-1 votes
1 answer
812 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 ...
Zizogolu's user avatar
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3 votes
1 answer
1k 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 ...
ceno980's user avatar
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1 vote
1 answer
607 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: ...
ceno980's user avatar
  • 159
1 vote
1 answer
1k 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 ...
ceno980's user avatar
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2 votes
1 answer
8k views

Changing the order of colors in pheatmap

I plotted a heatmap I want cancer to be red and healthy to be blue ...
Zizogolu's user avatar
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1 vote
0 answers
25 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. ...
dunkindonts's user avatar
0 votes
1 answer
2k 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 ...
Mahta Mira's user avatar
0 votes
1 answer
2k views

Seurat heatmap for two conditions

I have a Seurat object of four cancers and four controls ...
Mahta Mira's user avatar
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1 answer
3k 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. ...
Dahlia's user avatar
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1 answer
2k views

I want to display color key on my heatmap

...
Aranyak Goswami's user avatar
3 votes
1 answer
2k 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 ...
Reza Rezaei's user avatar
0 votes
1 answer
286 views

Adding legend to Botton and top annotation in complexheatmap

I have a heat map but top and bottom annotation don't have legend ...
Zizogolu's user avatar
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0 votes
1 answer
113 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 ...
John Abercrombie's user avatar
1 vote
3 answers
3k 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 ...
Dan's user avatar
  • 136
2 votes
1 answer
2k 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 ...
rodrigarco's user avatar
-2 votes
1 answer
128 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 ...
Zizogolu's user avatar
  • 2,132
-4 votes
1 answer
65 views

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

I have a data frame ...
Zizogolu's user avatar
  • 2,132
1 vote
1 answer
601 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 ...
user98059's user avatar
  • 347
0 votes
0 answers
369 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 ...
Rycon's user avatar
  • 11
1 vote
0 answers
4k 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 ...
Rycon's user avatar
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1 vote
0 answers
128 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 <...
Jordan's user avatar
  • 11
3 votes
2 answers
693 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 ...
beginner's user avatar
  • 631
1 vote
1 answer
7k 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 ...
Ramsey Najm's user avatar
-1 votes
1 answer
79 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 ...
Zizogolu's user avatar
  • 2,132
1 vote
1 answer
728 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 ...
Ram RS's user avatar
  • 2,279
2 votes
2 answers
4k 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 ...
Charles's user avatar
  • 537
2 votes
1 answer
2k 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 ...
kcm's user avatar
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2 votes
0 answers
1k 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 ...
kcm's user avatar
  • 1,794
2 votes
1 answer
3k 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....
Zizogolu's user avatar
  • 2,132
7 votes
3 answers
6k 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 ...
Zizogolu's user avatar
  • 2,132
2 votes
0 answers
116 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 ...
Anna1364's user avatar
  • 516