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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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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  • 117
3 votes
0 answers
25 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. ...
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  • 355
3 votes
1 answer
38 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 ...
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3 votes
2 answers
187 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. <...
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3 votes
2 answers
56 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 - ...
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2 votes
0 answers
31 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 ...
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  • 539
0 votes
1 answer
62 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 ...
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  • 101
2 votes
1 answer
45 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 ...
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3 votes
0 answers
45 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 ...
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1 vote
1 answer
40 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 ...
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  • 1,538
2 votes
0 answers
12 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 ...
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-1 votes
1 answer
22 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 ...
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  • 53
0 votes
1 answer
241 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 ...
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1 vote
0 answers
89 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 vote
1 answer
43 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 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 ...
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2 votes
1 answer
143 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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  • 23
1 vote
1 answer
37 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 ...
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  • 2,099
1 vote
0 answers
32 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 ...
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1 vote
0 answers
36 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 ...
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2 votes
1 answer
111 views

Create identicon of a DNA sequence

How can I create an identicon (a visual representation) of a DNA sequence?
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  • 2,564
2 votes
1 answer
129 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 ...
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  • 23
0 votes
2 answers
46 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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  • 11
1 vote
1 answer
164 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........... ...
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1 vote
3 answers
2k 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 ...
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  • 36
1 vote
1 answer
79 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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  • 539
1 vote
4 answers
128 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 ...
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  • 1,363
-1 votes
2 answers
318 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 ...
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  • 1,513
2 votes
1 answer
212 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 ...
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3 votes
1 answer
465 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 ...
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  • 7,957
0 votes
1 answer
174 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 ...
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  • 127
5 votes
4 answers
256 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 ...
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  • 2,224
0 votes
0 answers
27 views

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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2 votes
1 answer
86 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 ...
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  • 121
1 vote
2 answers
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 ...
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  • 123
1 vote
1 answer
92 views

Error Viewing file on HiGlass

I am implementing hi-glass python on Jupyter, and upon running the test data code ...
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3 votes
1 answer
2k 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 ...
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  • 7,957
2 votes
1 answer
2k 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, ...
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  • 21
3 votes
1 answer
90 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 ...
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  • 1,538
2 votes
2 answers
732 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 ...
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  • 143
5 votes
1 answer
249 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 ...
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0 votes
1 answer
436 views

Mutation annotation to the heatmap

I have mutation data of patients.How do i add that mutation info or annotate those as column with my annotation information expression and mutation To help myself i did try this Zuguang Gu but couldn;...
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  • 1,538
4 votes
2 answers
478 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 ...
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  • 325
2 votes
1 answer
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 ...
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  • 1,538
2 votes
0 answers
240 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 ...
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  • 1,538
3 votes
1 answer
376 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 ...
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  • 1,181
5 votes
2 answers
143 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 ...
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2 votes
2 answers
48 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 ...
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2 votes
1 answer
1k 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: ...
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  • 1,538
2 votes
0 answers
545 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 ...
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  • 1,538