13 votes
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Using the t-SNE algorithm on microarray data + an error bonus

Converting your data.frame to a matrix (and then removing the data.frame) will often free up ...
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13 votes
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Volcano plot in R

This plot is clearly done using core R functions. There are smoother alternatives how to make a pretty volcano plot (like ggplot with example here), but if you ...
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  • 5,287
6 votes

Interpreting Intergrative Genomic Viewer (IGV)

You've apparently colored your alignments by read strand. In this case, red indicates "+ (watson) strand" and blue indicates "- (strand) strand". This strand association is determined by the ...
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6 votes
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Visualization tools for 3C/Hi-C long-range interaction data?

I would also recommend two very recent Hi-C visualization frameworks (with some public data available in both): HiGlass and JuiceBox.
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  • 176
6 votes
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full visualisation of draft genomes alignment

Found a solution, using D-Genies, worked great. Some examples from their website: Thanks to @user172818.
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  • 2,614
6 votes
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What is the name of this type of figure?

This kind of visualization showing the banding patterns of chromosomes are called "chromosome ideograms". You can use for example IdeoViz in R to generate them.
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  • 788
5 votes

How to enlarge a section of y-axis?

I would strongly discourage you from making discontinuous axis, it's going to be very confusing for a reader. The facet plot you proposed seems like a good solution to me. Alternatively you can use ...
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  • 5,287
5 votes

Visualisation of long read RNA-Seq splicing

DNASTAR's software is for purchase, but high quality. GenVision Pro does genomic visualization, including Sashimi plots. Edit: not sure why this answer is being downvoted, unless it's because the ...
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5 votes

A good tool for gene locus visualization

I think in R, Gviz is the best choice. I have used it for human sequences but it will probably also be suitable for Prokaryotes. Another option is MS powerpoint, if you only need the arrows...
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  • 3,521
5 votes
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What do the read colors in IGV mean?

Could it be that these are reads with their mates found on other chromosomes? That's the part of the IGV documentation which seems to make sense in this context: for paired end reads that are coded ...
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  • 1,378
5 votes

Need a alternative or more complex version of venn diagram in python for matching dna sequences

To get around limitations in using Venn diagrams for set overlaps, when there are more than three sets, back around 2013 or so I created something I called an Eulergrid plot (example at the bottom of ...
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5 votes

Create identicon of a DNA sequence

Sequenticon is a Python library for generating identicons for DNA sequences. For instance, the sequence ATGGTGCA gets converted into the following icon: A web ...
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  • 2,564
4 votes
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Highlight CpG sites with Texshade

The best solution I could find was to use the \shaderegion function on all the sequences so it ended up looking something like this: ...
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  • 255
4 votes
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creating graph of distribution of blast hits on the query sequence

You probably want to include query start (qstart) and query end (qend) in your blast output. Something like this: ...
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  • 3,521
4 votes
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Customizing bigWig file

There's no equivalent to the wiggle header in bigWig (or bigBed) files, which is why UCSC uses the file name. This is actually the reason for the track line stuff that you linked to, since you can ...
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4 votes
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3D PCA group labelling

You can easily color 3D pca plots in R based on the code given below: ...
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4 votes
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Extracting genes from corrplot and adding labels based on high and low corelation

Here is a solution using the pheatmap library to cluster and visualise the correlation matrix, then extract the groups from the cluster dendrograms: ...
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4 votes

Visualize similar interactions in two homologous networks

An easy way to visualize this is to make a tab-delimited table that contains edge information for both species and both networks, color the edges depending on the species, and make the thickness and ...
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  • 3,061
4 votes
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Occupancy of TFs with the target genes

I would ignore peak calling for this and instead compute enrichment of ChIP/input for the genome (e.g., with deepTools or presumably homer) and then plot it for the genes of interest individually (e.g....
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3 votes

Seurat Merged objects tSNE - How to paint on original IDs?

Below a few lines of code that accompany BC Wang's answer. After using MergeSeurat the sample name will be added to meta data under orig.ident. this can then be used to color the tSNE either using ...
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3 votes

Volcano plot in R

Without a minimal reproducible example (MWE), I can't reproduce the plot but I would suggest using existing volcanoplot functions such as the ...
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  • 873
3 votes
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Visualisation of long read RNA-Seq splicing

IGB gives the intended result without much hassle. It doesn't have the bells and whistles of IGV, but presents a clean and intuitive view of the individual reads. In IGB, each read is presented as a ...
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3 votes

Visualisation of long read RNA-Seq splicing

The Sashmi Plot feature built into IGV. It gives a nice summary of the spliced transcripts and the coverage of each exon. For example:
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  • 727
3 votes

Visualization tools for 3C/Hi-C long-range interaction data?

If you have more than a dozen or even hundreds of regions that you want to compare you could check a companion tool of HiGlass called HiPiler. HiPiler lets you arrange, cluster, and pile up to ...
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3 votes

A good tool for gene locus visualization

gggenes is a ggplot2 based solution and looks very appealing. Plus, it has a nice introduction with examples. ...
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  • 41
3 votes
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A good tool for gene locus visualization

I ended up using Easyfig, which is made for the task and requires little tinkering around, once fed the genbank files. (Granted, being so simple, it's hard to make the image more advanced, but it ...
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  • 101
3 votes

A good tool for gene locus visualization

GFF2PS was developed for exactly this sort of thing. It takes a GFF file as input, and will produce a pretty PS output showing the annotations. It was used to create the poster for Celera's human ...
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  • 7,957
3 votes
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How to plot p-values in a circular barplot?

The adjustcolor function from grDevices can be used to generate colours with transparency. What you want is colours based on the ...
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  • 873
3 votes
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Plotting coverage of annotation over collection of region

If one assumes that repeat elements of a given type (e.g., LINEs) don't overlap each other, then the following will work: Split your BED file by repeat element, such that you have a LINE.bed, SINE....
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3 votes

What is the name of this type of figure?

Such a figure is called ideogram, or chromosome ideogram.
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