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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2
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1answer
41 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
18 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 ...
3
votes
2answers
54 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 ...
0
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0answers
18 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
39 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 ...
1
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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 ...
1
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1answer
20 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
137 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
votes
1answer
244 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, ...
0
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0answers
21 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
votes
1answer
59 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
votes
2answers
124 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
81 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
125 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;...
0
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1answer
65 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
votes
2answers
191 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
441 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
85 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
votes
1answer
128 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
votes
2answers
69 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
324 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
239 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 ...
1
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0answers
304 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
311 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
71 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 ...
0
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1answer
38 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
votes
2answers
254 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
412 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
votes
1answer
788 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
votes
1answer
125 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 ...
4
votes
3answers
956 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 ...
-1
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1answer
114 views

Boxplot of kmean cluster

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0
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1answer
59 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, ...
0
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0answers
201 views

Making a plot cleaner

By this code I produced this tSNE ...
1
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0answers
162 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
votes
1answer
122 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
141 views
3
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1answer
106 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
vote
1answer
77 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
votes
0answers
501 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 ...
0
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0answers
57 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
votes
1answer
245 views

How to enlarge a section of y-axis?

I am using ggplot2 to plot a scatter plot. ...
6
votes
3answers
4k 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.
5
votes
3answers
229 views

A good tool for gene locus visualization

Does anyone know of a good tool for visualizing gene loci? Basically, I'd like to show how a group of genes look in different strains of a bacteria. I have annotation of course, I just need a tool to ...
1
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0answers
103 views

igv_plotter error: Xvfb did not start

I am trying to get screenshots from alignments of reads to a genome in IGV (Integrated Genome Viewer) using igv_plotter. ...
2
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0answers
46 views

Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein. The trajectories are from my Gromacs simulation. Firstly I use ...
1
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0answers
56 views

Can I batch output the graph of Secondary Structure in VMD Timeline analysis?

I am using the VMD software, and use "Extension - Analysis - Timeline - Calculate - Calc. Sec. Structure" to visualise the secondary structure of my trajectories. I need to screenshot to get the ...
1
vote
1answer
186 views

Histogram of different classes of variables in one column [closed]

I have a basic ggplot2 R question. I have a dataframe in which data looks like this: AA 4 AA 6 BB 6 AB 5 BA 4 AA 3 NN 2 AN 6 NN 5 AN 4 NA 3 BB 6 BN 5 NB 1 BN 7 ...
3
votes
1answer
51 views

Highlight CpG sites with Texshade

I am using Texshade to produce figures for MSA. Upon reading the documentation I could not find anyway to highlight how conserved CpG sites within the alignment. Does anyone know if this is possible? ...