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.
93
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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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1
vote
1
answer
92
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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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2
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62
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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
1
vote
1
answer
38
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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
votes
2
answers
55
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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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1
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150
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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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1
vote
1
answer
171
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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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1
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309
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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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2
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2
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262
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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 ...
- 301
1
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1
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70
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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, ...
- 301
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52
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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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3
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71
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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
4
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2
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9k
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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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3
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1
answer
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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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3
votes
1
answer
332
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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 ...
- 153
3
votes
2
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540
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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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4
votes
2
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83
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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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2
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0
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70
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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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1
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181
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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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2
votes
1
answer
87
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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 ...
- 151
3
votes
0
answers
264
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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 ...
1
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1
answer
53
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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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0
answers
13
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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 ...
-1
votes
1
answer
46
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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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1
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606
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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 ...
1
vote
0
answers
277
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 ...
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1
answer
129
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
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1
answer
32
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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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2
votes
1
answer
373
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:
...
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1
vote
1
answer
61
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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 ...
- 2,139
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0
answers
40
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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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0
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40
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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 ...
- 381
2
votes
1
answer
116
views
Create identicon of a DNA sequence
How can I create an identicon (a visual representation) of a DNA sequence?
- 2,604
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1
answer
190
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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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0
votes
2
answers
90
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 ...
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1
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1
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239
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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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1
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3
answers
2k
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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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1
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158
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 ...
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4
answers
328
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 ...
- 1,373
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2
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461
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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 ...
- 1,801
2
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1
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348
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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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1
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863
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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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0
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1
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331
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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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4
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306
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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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0
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31
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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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1
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101
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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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2
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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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1
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147
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Error Viewing file on HiGlass
I am implementing hi-glass python on Jupyter, and upon running the test data code
...
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1
answer
3k
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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 ...
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1
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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, ...
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