Questions tagged [heatmap]
The heatmap tag has no usage guidance.
39 questions
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What is the significance of the weak inferCNV signal in non-malignant cells in culture that underwent scRNA-seq?
I'd be grateful for an opinion on the attached infercnv heatmap as InferCNV Github support has been paused. We performed scRNA-seq on human induced pluripotent stem cell (iPSC)-derived brain organoids ...
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1
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2k
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Manually set range of colour scale in PHeatmap in R
I'm using pheatmap to generate a correlation matrix in R. Ideally, I want my colour scale to run from -1.0 - 1.0 but my lowest negative correlation is 0.6. Is there a way to manually set the range?
<...
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131
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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
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3
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1
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213
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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 ...
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124
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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. ...
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2
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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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1
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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
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561
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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
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1k
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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 ...
- 2,232
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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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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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2k
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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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1
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10k
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Changing the order of colors in pheatmap
I plotted a heatmap
I want cancer to be red and healthy to be blue
...
- 2,232
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27
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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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1
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3k
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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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3k
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1
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1
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3k
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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
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2k
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3
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1
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2k
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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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1
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370
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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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- 2,232
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1
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130
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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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3
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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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1
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2k
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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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130
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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 ...
- 2,232
-4
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1
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70
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How to visualise the proportion of clonal genes to sub clonal genes [duplicate]
I have a data frame
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- 2,232
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1
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782
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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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- 347
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423
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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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5k
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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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0
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136
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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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2
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870
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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
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8k
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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
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81
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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
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1
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760
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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
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4k
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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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1
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2k
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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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1k
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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
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3k
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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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3
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7k
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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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124
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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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