Questions tagged [heatmap]

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31 views

plot transcript expression vs length

I am working on long read RNA sequencing. I am interested in looking whether there is any bias on shorter gene against longer genes in my data as well as whether any bias towards 5' or 3' ends. Oneway ...
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1answer
329 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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1answer
91 views

I want to display color key on my heatmap

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3
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1answer
559 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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1answer
95 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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1answer
34 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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3answers
654 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 ...
2
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1answer
595 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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1answer
120 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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1answer
61 views

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

I have a data frame ...
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0answers
122 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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0answers
165 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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0answers
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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0answers
94 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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2answers
142 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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1answer
3k 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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1answer
60 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 ...
1
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1answer
460 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 ...
2
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2answers
2k 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 ...
2
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1answer
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 ...
2
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0answers
790 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 ...
2
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1answer
1k 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....
6
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3answers
4k 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 ...