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.
96
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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 ...
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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 ...
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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 ...
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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 ...
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196
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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 ...
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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
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54
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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)
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2
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68
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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 (...
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319
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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 ...
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293
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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?
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331
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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.
...
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385
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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 ...
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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, ...
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55
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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 ...
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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
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Error in seaborn plot " Horizontal orientation requires numeric `x` variable"
I am trying to plot a box plot with seaborn with the following code
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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.
...
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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 ...
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732
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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.
<...
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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 -
...
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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 ...
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272
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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 ...
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107
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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 ...
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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 ...
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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 ...
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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 ...
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1
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119
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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 ...
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756
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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 ...
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0
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380
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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 ...
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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
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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 ...
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527
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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:
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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 ...
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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 ...
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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 ...
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119
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Create identicon of a DNA sequence
How can I create an identicon (a visual representation) of a DNA sequence?
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216
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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 ...
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2
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108
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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 ...
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269
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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........... ...
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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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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 ...
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4
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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 ...
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515
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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 ...
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456
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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 ...
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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 ...
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413
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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 ...
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345
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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 ...
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How to visualise /add Arabidopsis T-DNA Lines As Tracks On IGV
We have done some RNA-Seq on Arabidopsis T-DNA lines and mapped the reads on to Arabidopsis genome. Now we wanted to confirm the T-DNA deletion of those lines by loading them on IGV. As a control we ...
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107
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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 ...
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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 ...
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