Questions tagged [visualization]

use for questions regarding plotting and representation of data, combine with tags specific to type of analyses (genome, protein, rna-seq) and language or library (python, R, ggplot2, igv) if applicable. You are welcome to upload a sketch or a scheme of desired outcome.

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9
votes
3answers
550 views

Visualisation of long read RNA-Seq splicing

I have a dataset of Oxford Nanopore cDNA reads. Many of my reads are full-length or close to full-length transcripts, and I and am interested in examining alternative splicing. For this, I would like ...
7
votes
1answer
970 views

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

I'm trying to use the t-SNE algorithm on some microarrays data. More specifically my data frame has 18600 columns with genes (features) and 72 rows with conditions with replicates ( 10xWt , 10xTg , ...
7
votes
1answer
620 views

Interpreting Intergrative Genomic Viewer (IGV)

I was following a tutorial on "Tuxedo Genome Guided Transcriptome Assembly Workshop" and was wondering how to interpret the following: From what I understand from 'Color Legends', the color blue ...
6
votes
3answers
8k views

Volcano plot in R

This question has also been asked on biostars How can I reproduce this volcano plot? I'm only able to do the traditional one, I'm kind knew too these field.
6
votes
4answers
477 views

A good tool for gene locus visualization

Does anyone know of a good tool for visualizing gene loci? Basically, I'd like to show how a group of genes look in different strains of a bacteria. I have annotation of course, I just need a tool to ...
6
votes
3answers
212 views

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

I have identified a genomic region (CpG island) that is enriched for a characteristic of interest in the vast majority of my samples. After viewing it in the UCSC genome browser, I have confirmed ...
5
votes
2answers
565 views

full visualisation of draft genomes alignment

I have two draft genomes (aprox. 500Mb each), one with ~10'000 scaffolds (genome1.fasta) and one with ~1'000 contigs (...
5
votes
3answers
2k views

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

I am working with single-cell RNA-seq data, using the R package "Seurat" to cluster and visual data-points. I had two single cell datasets from which I generated two Seurat objects. I then combined ...
5
votes
1answer
957 views

creating graph of distribution of blast hits on the query sequence

I'm attempting to visualize the results of my BLAST search in a way similar to the graphical display of the distribution of blast hits from the web BLAST. For example, from my BLAST search: except I ...
5
votes
1answer
312 views

Customizing bigWig file

I generate bigWig files using bamCoverage from deeptools, in part for my colleagues to visualize their mapped libraries in the IGV viewer. A problem is that the ...
5
votes
2answers
129 views

Control width of samtools tview "snapshot" when redirecting

I have a large number of loci I would like to examine manually with samtools tview. Rather than typing or copy-n-pasting dozens of coordinates, I was hoping to ...
5
votes
4answers
223 views

tool to visualize a collection of phylogenetic trees

I have a collection of phylogenetic trees produced from clustering DNA sequences, mostly a few nodes in each cluster/tree, with several clusters of size 1. And I would like to visualize them all ...
4
votes
1answer
954 views

How to enlarge a section of y-axis?

I am using ggplot2 to plot a scatter plot. ...
4
votes
2answers
412 views

Plotting coverage of annotation over collection of region

I'm trying to plot "meta" coverage of annotation: i.e. features (eg. gene class) over certain regions. It is similar to read coverage plots over gene body, except my input is two bed files (both in ...
4
votes
1answer
614 views

How to plot p-values in a circular barplot?

Im trying to plot reactome pathway in for of circular bar plot using ggplot2 my data ...
4
votes
1answer
297 views

Plot to show the expression of genes between tumor and normal

I have RNA-seq raw counts data for 50 samples. 20 Normal and 30 tumor. After differential analysis I got 30 DEGs. I want to make a violin plot showing the expression of each gene. I transformed counts ...
4
votes
1answer
140 views

Tool to show DNA sequence and allowing upload of own graph data

Background We want to be able to load (or request) data for a genome including the sequence and gene annotation (bacteria). Then, we want to load our own annotation which should be displayed as a ...
4
votes
1answer
201 views

Displaying soft-clipped nucleotides in samtools tview

There are nicer genomics visualization tools available, but the samtools tview command is almost always my go-to for a quick first look at read alignments. I just ...
3
votes
1answer
1k views

What do the read colors in IGV mean?

I was looking at a bam file in the IGV viewer and saw: What do the different read colors mean? Why is one read a light blue color, another green, another aquamarine (?), another purple and another ...
3
votes
1answer
82 views

Occupancy of TFs with the target genes

The occupancy of SMARCD3 in the target genes listed below. I want to see average, normalized ChIP-seq signal at the promoter proximal region (1000bp upstream and downstream of the TSS). I have 4 ...
3
votes
1answer
54 views

Highlight CpG sites with Texshade

I am using Texshade to produce figures for MSA. Upon reading the documentation I could not find anyway to highlight how conserved CpG sites within the alignment. Does anyone know if this is possible? ...
3
votes
1answer
320 views

How can I export a full alignment from IGV as an image?

The IGV browser lets you export an alignment as an image (File => Save Image). However, this image only contains those reads that fit in the viewing window: As you can see in the image above by ...
3
votes
1answer
329 views

How to plot genomic.fna fasta file in R using Gviz?

I downloaded the genome of Staph aureus as DNA sequence from NCBI. I would like to visualize it using Gviz. Is Gviz the right tool to visualize genomes? What are the necessary steps from the sequence ...
3
votes
1answer
247 views

How to remove frame on RDKit figures?

RDKit can plot molecules, thought the structures are surrounded by an ugly frame with ticks. How can I turn that off and plot the molecules without that frame? Note, the ...
3
votes
1answer
231 views

Error in seq.default in chromPlot

I am using chromPlot to visualise the genome of C. elegans. library(chromPlot) I have created the following data frame with the lengths of C. elegans chromosomes. ...
3
votes
0answers
83 views

Can VMD change its cartoon representation for secondary structure according to trajectories? [closed]

I am using VMD to visualise the secondary structure of protein here. The trajectories are from my Gromacs simulation. Firstly I use ...
2
votes
1answer
106 views

Create identicon of a DNA sequence

How can I create an identicon (a visual representation) of a DNA sequence?
2
votes
2answers
45 views

Visualize similar interactions in two homologous networks

Background I have two networks with homologous genes from two different species. To identify homologs I performed a functional comparison. One of the species is not well studied while the other one is ...
2
votes
1answer
939 views

Extracting genes from corrplot and adding labels based on high and low corelation

I am doing a gene-gene pairwise correlation, I get a plot and I do see positive and negative correlation My code: ...
2
votes
1answer
2k views

3D PCA group labelling

I would like to make a 3D PCA but not sure how to label group wise which i can do for 2D PCA ...
2
votes
1answer
96 views

Survival analysis using CoxPH - Effect of covariates

Hi and sorry for the long post in advance, I'm doing a survival analysis of lung cancer patients using Python's lifelines package. According to the documentation, the function ...
2
votes
1answer
156 views

How can I not show insertions in the Integrative Genome Viewer (IGV)?

I am using IGV 2.5.2 and would not like to see the insertions in my aligned reads. How can I do that? I have managed to remove mismatched bases because there is an option to do so when I right-click ...
2
votes
1answer
89 views

How do I plot clusters based on DNA sequence alignment?

I have a group of about 1050 sequences that have been aligned using blastn. I am now trying to create a cluster plot of the sequences in order to identify similar sequences, something like this: ...
2
votes
2answers
610 views

Loading local FASTA file in igv.js

I'm trying to use igv.js for a very simple visualization of some genomic alignments, but I can't get past the first step. I have a FASTA file that I want to use as the reference, but igv.js ...
2
votes
1answer
58 views

Visually summarizing phylogenetic networks

After having worked with Bayesian phylogenetic tree inference for some time, I am now trying out a method to infer network phylogenies. To get an idea of what it infers, I'd like to find a way of ...
2
votes
1answer
1k views

How to highlight specific cells in Seurat 2.4

I used Seurat 2.4 on our scRNA dataset to obtain the following tSNE plot.I was able to successfully extract cell IDs from the different clusters, and generate gene expression profiles. The analysis, ...
2
votes
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
votes
1answer
1k views

Plotting gene models - alternatives to ggbio

I am curious how people make genome track plots such as what can be done with the Bioconductor package ggbio. For example this plot was made w/ ggbio: I think ...
2
votes
0answers
196 views

Ploting FDR along with the pathway as heatmap any simple way

I have this data from one of the cluster which show pathway in context of those genes but when i do a bit of filtering i see plenty of pathways with same or similar FDR which are sort of redundancy i ...
2
votes
0answers
470 views

corrplot issue with correlation plot output

Very conceptual doubt not sure if im doing it right or something terribly wrong so im using this corrplot library to calucate the correlation of my desired data frame after that i rounding it off but ...
2
votes
0answers
869 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 ...
1
vote
2answers
1k views

What is the name of this type of figure?

This figure comes from this wiki page. I googled "gene location figure" and "gene location plot", none gets similar results. I also tried search by image, none of the results is close. so, what is ...
1
vote
4answers
78 views

Tools for comparing/visualizing FASTAs?

I have two FASTAs/assemblies of the same species, but the bases are somewhat different. I would like to explore this. What tools/methods exist to compare two FASTAs and see the difference in ...
1
vote
1answer
125 views

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

I am in google colab and I have combined and set up a data frame list of sequences that goes like this Location ID Sequence 1.1 ........ A ........ AAGAGATA 1.2 ........ A........... ...
1
vote
1answer
32 views

Is SBOL-VOWS operational?

Synthetic Biology Open Language's Visual Ontology Webservice docs have example URLs but they all return a github pages 404. EDIT: The SBOL-VOWS has site has been fixed but the section on the SBOL ...
1
vote
3answers
980 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 ...
1
vote
1answer
30 views

Phylogenetics software that can represent collapsed nodes as triangles

I am trying to represent a large (100-300+ sequences) phylogenetic tree in a way that gets my point across. I figured that reducing the number of branches (by collapsing clades which include highly ...
1
vote
1answer
118 views

How to superimpose barplots in karyotype graphic using the chromPlot Bioconductor package?

I have a data frame containing 4 columns: Chrom: chromosome name of the feature Start: starting base of the feature End: end base of the feature Name: name of the feature, e.g. 5S ribosomal RNA The ...
1
vote
1answer
355 views

Histogram of different classes of variables in one column [closed]

I have a basic ggplot2 R question. I have a dataframe in which data looks like this: AA 4 AA 6 BB 6 AB 5 BA 4 AA 3 NN 2 AN 6 NN 5 AN 4 NA 3 BB 6 BN 5 NB 1 BN 7 ...
1
vote
1answer
26 views

Label and labelbox mismatched in Pymol after ray

I would like to ask how to overcome the problem of mismatched boxes and labels (pic). Is there an option focused on this? thanks Radim