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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1answer
14 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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0answers
17 views

Free, user-friendly software for visualizing and comparing gene clusters?

I'm looking for a tool to do the job listed in the title. I've come across Gene Graphics (https://academic.oup.com/bioinformatics/article/34/8/1406/4708234), but never used it and I was wondering if ...
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0answers
3 views

How do you select only alpha carbons in a graphical representation in VMD?

I am trying to select only alpha carbons for one protein, and I'm getting into a lot of trouble. My OS is Windows 10. The most recent thing I have tried is type in the Selected Atoms bar "name CA." I ...
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3answers
48 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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2answers
57 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 ...
2
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1answer
45 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 ...
3
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1answer
87 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 ...
0
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1answer
25 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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4answers
118 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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0answers
23 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 ...
2
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1answer
45 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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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 ...
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1answer
39 views

Error Viewing file on HiGlass

I am implementing hi-glass python on Jupyter, and upon running the test data code ...
3
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1answer
386 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 ...
2
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1answer
584 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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0answers
41 views

How to order grouped elements in Gviz

Gviz is useful for visualization of gene transcripts by genomic coordinates. I'm using it to show the difference between splice variant transcripts. However, it seems that the ordering of transcript ...
3
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1answer
68 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 ...
2
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2answers
225 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 ...
4
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1answer
110 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 ...
0
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1answer
179 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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1answer
82 views

Extracting modules from corelation and then module clustering

This is the paper where they have first done co-expression analysis of TF and then found coexpressed modules which were further subjected to module clustering ,paper So now im clear about the first ...
4
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2answers
267 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 ...
2
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1answer
724 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
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0answers
126 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 ...
3
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1answer
189 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 ...
5
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2answers
88 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 ...
2
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2answers
42 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 ...
2
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1answer
513 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
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0answers
313 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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0answers
423 views

How to plot a 2D RNA structure in python using dot-bracket input?

I need some help with forgi library for visualisation of RNA secondary structure. I have an RNA sequence and dot-bracket notation of the secondary structure and I would like to plot 2D graph like ...
4
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1answer
421 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 ...
3
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1answer
123 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 ...
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1answer
47 views

How to create a graph of multi column gene dataset?

well, I'm new to Bio. what I'm going to do is create a network/graph of a dataset related to the genes I think. here's the sample of the nodes dataset with CSV format named lung-nodes : and this is ...
5
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2answers
363 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 (...
2
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0answers
545 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 ...
2
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1answer
1k 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 ...
4
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1answer
133 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 ...
5
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3answers
1k 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 ...
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1answer
227 views

Boxplot of kmean cluster

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1answer
83 views

Visualize network (graph) using “line” layout

I want to visualise a network in a way that the nodes are along a line (and the edges are not on that line). I have included a simple example below. Which network visualisation programs (Cytoscape, ...
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0answers
207 views

Making a plot cleaner

By this code I produced this tSNE ...
1
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0answers
232 views

How to make year scale bar unit in figtree software?

I have generated phylogenetic trees for virus sequences by using beast software. I observed in various research articles that the phylogentic trees also have a scale-bar (which mostly represents ...
4
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1answer
167 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 ...
0
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1answer
195 views
3
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1answer
142 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. ...
1
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1answer
94 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 ...
2
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0answers
643 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 ...
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0answers
72 views

“Cleaning up” a gene heatmap in R

I'm using the ComplexHeatMap function from Bioconductor to display a heatmap showing the presence/absence of hundreds of loci of interest, but I need to clean it up ...
4
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1answer
429 views

How to enlarge a section of y-axis?

I am using ggplot2 to plot a scatter plot. ...
6
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3answers
6k 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.