Questions tagged [ggplot2]

R visualisation and plotting package based on the grammar of graphics. ggplot is also available in Python.

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How do I add a colour annotation bar to the heatmap generated by DoHeatmap function of Seurat v2?

I am using Seurat v2 for professional reasons (I am aware of the availablity of Seurat v3). I am clustering and analysing single cell RNA seq data. How do I add a coloured annotation bar to the ...
2
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0answers
78 views

How to plot gene mutation frequencey in terms of percnatge alteration in samples?

I'm taking data from cbioportal of gene and their mutation frequency with percentage which I'm trying to categorize with various sub class. The issue I'm facing is I have to plot it in mutation ...
2
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0answers
566 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 ...
1
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1answer
160 views

Ternary plot in R

I have plotted a triangular plot,that three dimensions of which represent three herbal strategies. One dimension represents the strategy of C (competitive plant), the second dimension “S” (stress ...
1
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0answers
55 views

How can I correctly get 3D scatter plot for micro-array pheno data in R [updated]?

I intend to see data points distribution (each reows) within labeled groups (different batchs such as 1,2,3, and so on) in 3D scatter plot, because I want to see the distribution of the data points ...
1
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0answers
151 views

How to create a dendrogram of clusters and reconstruct phylogenetic relationship

I'm working with a Daphnia data set looking at the 16s gene pulled from the BOLD database. So far I did a multiple sequence alignment and attempted to cluster and plot a dendrogram: ...
1
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0answers
79 views

Ordering the cells by the expression of specific genes

I have 209 cells. I want to show the expression of two genes by ordering my cells. Imagine something like a plot on which y axis shows the read counts range from 0 to 10000 and x axis shows the number ...
0
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0answers
31 views

What means the negative sign on the colour scale when I use Seurat's DotPlot function to visualise gene expression in single cell rna seq data?

I wish to find out the meaning of the values on the average expression scale when one uses the Seurat DotPlot. If the scale represents the average expression per feature plotted per identity class, ...
0
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0answers
32 views

How to set equal distances between axes ticks irrespective of number of points I plot in a ggplot?

how can I set an equal distance between the ticks of axes in a ggplot irrespective of the number of items I plot? For example I want to have the kind of plot below from Seurat's ...