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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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Are there efficient tools for PANGENOMES visualization (size >1Gbp)?

I've been looking for a program that allows me to visualize pangenomes efficiently and it has been very difficult find satisfactory documentation about large pangenome's visualization tools since most ...
AIsaac's user avatar
  • 21
2 votes
0 answers
31 views

Method for reproducing minimal, cartoon-style protein structure visualisation

I recently came across a preprint ( DOI, PDF link ) that has some figures of protein structures in a style that I have not seen before. To me it appears easier on the eyes and less noisy than the ...
asimov's user avatar
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0 votes
0 answers
8 views

Where would I get the activity profile dataset for Lantus Solostar insulin, and for other diabetes treatments such as Metformin?

I am working on a personal project for a better, more informed management of my own Diabetes Mellitus, Type 2 (aka "T2DM", or "T2D"). With some difficulty I am able to access and ...
Fritt Ro's user avatar
1 vote
1 answer
675 views

Changing transparency of markers in Chimera X

I am using the software Chimera X to visualize the 3d composition of molecules. I am very new to Chimera and only use it for visualization. The files I'm using are cmm files (xml-formatted) basically ...
ciru_4011's user avatar
1 vote
1 answer
54 views

Identifying the promoter on the reverse strand using visualization software (seqmonk)

I feel like this might be a really silly question and I've been going back and forth for awhile and I think confusing myself- so sorry if this is dumb. I am using Seqmonk to visualize genes in an ...
user18170's user avatar
1 vote
1 answer
67 views

What options are there for visualising DNA sequences?

I typically see several ways of visualising DNA sequences and I would like to know when (best) to use them? For example, I sometimes see the letter codes GATC, sometimes I see colours, sometimes I see ...
Scott McKenzie's user avatar
2 votes
1 answer
61 views

Using ticks on the x axis or a scale bar when visualisizing a phylogram?

When visuliazing a phylogram is it preferable to show ticks on the x axis or a scale bar? Given an example tree with branch lengths in newick format ...
Tony's user avatar
  • 43
1 vote
1 answer
255 views

variant visualisation of VCF files for 30+ samples

I am relatively new to genome analysis and would like to compare 30+ vcf files, 1 sample per file. After filtering there are about ~20 variants per vcf file. I would like to evaluate to mutational ...
Macintosh's user avatar
  • 160
0 votes
2 answers
183 views

Is there a tool to visualize RNA secondary structure?

I want to manually fold and pair two sequences (U4 and U6). And I want to make niceish figures. I haven't found a single program that does that. thanks
user3392394's user avatar
1 vote
1 answer
63 views

How to get single histogram plot for all groups in different colours?

I am using the below script to get the histogram plot for all values together. However, I want a single plot but different colours for different groups (A, B, C) ...
Tom Morgan's user avatar
2 votes
2 answers
90 views

To get background_gradient plot for all data frames in the for loop

I tried the below code to get the background_gradient plot for each diabetes_group. It is giving me only plot for the last group in the plot. How to get background_gradiant for all items (...
Megha's user avatar
  • 395
2 votes
1 answer
529 views

How to get separate histograms plots on the basis of the column value?How to detect which plot has most deviation?

I have a data frame (df) which has correlations calculated for different genes with respect to different ID combinations. I want to get separate histogram plot based on the gene name (separate plot ...
Riya's user avatar
  • 307
1 vote
1 answer
387 views

Visualize RNA co-folded secondary structure with Python

I would like to visualize the secondary structure of co-folded RNA strands in Python, preferably in a Jupyter notebook. What are the recommended tools? Can anyone provide an example?
Ita's user avatar
  • 111
3 votes
1 answer
342 views

How To display bar graph with error bars?

I am using the below code to get the bar plot. I want to get the bar plot with error bars displayed. ...
Megha's user avatar
  • 395
2 votes
2 answers
515 views

PWM (4xM matrices) to Sequence Logo Visualizations in MATLAB or Python

Is there a MATLAB, or else Python (not R) tool for visualizing sequence Logos from probability weight matrices (PWMs)? This seems like a basic and simple tool to implement, yet just above the ...
Zebra Fish's user avatar
1 vote
1 answer
73 views

Common tools for generating results and visualizations for bioinformatics and genomics publications

I am a computational scientist with background in computer science and engineering however very new to the field of bioinformatics and computational genomics. Looking at papers in nature, PLOS, Cell, ...
Zebra Fish's user avatar
0 votes
1 answer
57 views

statistical test and visualization of genes present in an experiment

I have a list of genes (n = 120) that are involved in breast cancer. And I have a list of differentially expressed genes (n = 70) that are present in the breast cancer gene list. My question is: Are ...
Mendel's user avatar
  • 75
0 votes
3 answers
101 views

How to make a network overlap of gene lists across 3 conditions like this image?

From 3 gene lists (lung, nasal, gut), how to make this gene overlap network plot? This image is figure 4a from: https://www.nature.com/articles/s41591-020-01227-z
user15597's user avatar
4 votes
2 answers
12k views

Error in seaborn plot " Horizontal orientation requires numeric `x` variable"

I am trying to plot a box plot with seaborn with the following code ...
Megha's user avatar
  • 395
3 votes
1 answer
1k views

Grouping x-axis in scatter plot

I am trying to plot one scatter plot for each group, where each group has continous values in x-axis. Reference Data Gives continuous x-axis but all groups are combined. ...
user98059's user avatar
  • 347
3 votes
1 answer
558 views

Suggestion for python graphics library to plot aligned protein sequences

I'm working towards developing some visualization method for multiple protein sequences and subsequences using PYTHON. I want to show the alignment of many fragment sequences to the original ...
The August's user avatar
3 votes
2 answers
911 views

Plotting a gene in Seurat

I saw in the extensive Seurat documentation for Dimplot (dimensional reduction plot), here, you can plot a gene by specifying it with group.by = "gene" but this does not work in practice. <...
Angus Campbell's user avatar
4 votes
2 answers
99 views

Arrange ggplot Figure for scRNA-seq data

I have generated a ggplot for 8 single-cell libraries, with the purpose of visualizing the tSNE facet plot by sample, colored by cell type -- with percentages. The best I could get to is this - ...
ShaniS's user avatar
  • 51
2 votes
0 answers
108 views

Does it make sense to compare the mean relative coverages for contigs / MAGs from samples that were not co-assembled?

I have a subset of high-quality MAGs from different environments, sequenced on different runs. I want to know, for any particular MAG, if it (or something similar to it) is present in any particular ...
Laura's user avatar
  • 927
0 votes
1 answer
332 views

Using different "principal components" in UMAP visualizations

In certain UMAP visualization, it appears that the visualizations show the first UMAP "principal component" plotted against the second. For example, like this: Apparently, this lets us use ...
Aaron's user avatar
  • 101
2 votes
1 answer
117 views

Visualization of mutations in (part of) viral genome - existing tools?

I'm trying to visualize mutations in SARS-CoV-2 sequences, somewhat like it's done on outbreak.info: but for individual sequences, probably on the base of the vcf files generated by the ARTIC ...
KeyboardCat's user avatar
3 votes
0 answers
556 views

How to analyze an IGV alignment

I'm working on a project where I am analyzing the performance of an alignment workflow. My goal is to find regions in the resulting BAM file where there are outstanding discrepancies or anything that ...
pythonbeginner44's user avatar
1 vote
1 answer
61 views

Peptide data visualization

I'm trying to replicate the figure given in this paper using this table which they have given. So what i understand from the figure is they have calculated the zscore between two condition and ...
kcm's user avatar
  • 1,804
2 votes
0 answers
19 views

How can I create a no-frills view config file for HiGlass?

Is there a basic example anywhere that explains how to create a no-frills view config to view the contact map for a non-human genome assembly using the server-based viewer at http://higlass.io? I ...
Rotwurg Nwossle's user avatar
-1 votes
1 answer
162 views

Why does my volcano plot show genes at the extremities of the graph?

I am confused about the genes at the top of the volcano plot. There are a lot of genes at the top, what's wrong with it? If that's normal what's the interpretation of it? I used volcano plot tools ...
Zahrae's user avatar
  • 63
0 votes
1 answer
905 views

PyMol: Output Polar Contacts Between Chains to Text File

I am new to PyMOL but have a very specific task that I need to do. I have a PDB structure file of protein homo-oligomer, and I want to use PyMol to determine polar contacts between chain A and all ...
Berk Yalcinkaya's user avatar
1 vote
0 answers
451 views

How to modify dot plot in MUMmer 3 for bacteria comparative genomics?

I was trying to make a dotplot to visualize genome-genome sequence alignment by using the MUMmer 3 software (it is typically used to compare whole genome sequences of bacteria). I runned the same ...
HelpNeederStudent's user avatar
1 vote
1 answer
224 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
Radim Jaroušek's user avatar
1 vote
1 answer
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 ...
Shamseen's user avatar
2 votes
1 answer
651 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: ...
Widget's user avatar
  • 23
1 vote
1 answer
80 views

Is there a difference between any scRNA-seq visualization and pseudotime?

Is there a good definition of pseudotime? Some tools are clearly labeled as pseudotime and produce values along a trajectory, but there are more complex approaches that involve branching and ...
burger's user avatar
  • 2,199
1 vote
0 answers
41 views

Java Protein Comparison Visualisation

I have project where I am required to build a visual analytics tool into an existing Java project to visually compare and analyse protein sequences from SwissProt, GenBank, EMBL etc. (downloaded from ...
user10169's user avatar
1 vote
0 answers
50 views

Analyzing and visualizing metagenomic data

I am starting out in metagenomics, Aim I wish to understand the whole analysis from the raw reads to interpretation. Background My current pipeline is used for: analyzing human gut microbiota cleans ...
Roger V.'s user avatar
  • 381
2 votes
1 answer
121 views

Create identicon of a DNA sequence

How can I create an identicon (a visual representation) of a DNA sequence?
Peter's user avatar
  • 2,634
2 votes
1 answer
243 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 ...
beerzy's user avatar
  • 23
0 votes
2 answers
117 views

Easy way to create gene plot in gviz?

I would like to create a simple plot of a given human gene containing the main features, e.g. exons, introns, ORFs, transcripts etc. I understand that gviz is a ...
Nereus's user avatar
  • 209
1 vote
1 answer
286 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........... ...
QueenBey'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
1 vote
1 answer
222 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 ...
Laura's user avatar
  • 927
1 vote
4 answers
849 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 ...
EB2127's user avatar
  • 1,423
-1 votes
2 answers
563 views

Making a boxplot or violinplot for several dataframe with different number of samples

I have 3 data frames for treatment of 3 different drugs and in each of them I have the number of mutation types like insertion, deletion, SNP and total of mutations for each patients. In each group I ...
Zizogolu's user avatar
  • 2,160
2 votes
1 answer
543 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 ...
Biomagician's user avatar
  • 2,459
3 votes
1 answer
1k 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 ...
terdon's user avatar
  • 10.2k
0 votes
1 answer
479 views

pymol script to only select 5 chains within a distance from a reference and save the selection

I am generating 30 asymmetric units of a protein structure. Now, I want to select different combinations of 5 units which are 30 Angstroms away from the reference and save it as a different file. Here ...
shome's user avatar
  • 147
5 votes
4 answers
377 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 ...
719016's user avatar
  • 2,324