Questions tagged [ggplot2]
R visualisation and plotting package based on the grammar of graphics. ggplot is also available in Python.
27
questions
0
votes
1answer
60 views
Changing the axis limits of ggplot objects
By EnhancedVolcano R package I have this plot with this code
...
2
votes
1answer
52 views
Create a Grouped Barchart
I’m trying to create a Group Chart like this:
I have 7 classes for each of 4 species, not 5 like in the diagram. I want to build i diagram to show the distributions of the classes in each species
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2
votes
1answer
101 views
Multiple line chart
I am trying to create a multiple coloured line graph based on six lines.
Essentially I have data that identifies different units of vegetation by the variable” NDVI (vegetation index)” I want to ...
1
vote
1answer
110 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
vote
0answers
39 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 ...
2
votes
1answer
365 views
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 ...
1
vote
0answers
38 views
Missing lower IQR in boxplot [closed]
Im not able to figure it out why the lower quartile of the two data points missing.
Data
Code
...
1
vote
1answer
153 views
Percentage distribution of cells in all clusters based on their treatment condition?
I have 2151 cells, I clustered them by Seurat to 5 clusters. With the code below, I am able to have the number of cells per cluster and per condition:
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3
votes
1answer
152 views
How do I prevent the FeatureHeatmap function from the Seurat package, from sorting my data groups in alphabetical order when plotting data?
How can I prevent a function from sorting my data groups (factors) in alphabetical order without affecting the integrity of the data? I am analysing single cell RNA sequencing data using Seurat 2.3.4. ...
2
votes
1answer
448 views
How to set the position of groups in a Seurat object on a FeatureHeatmap plot
I am analysing singe cell sequence data and I have followed this tutorial, https://satijalab.org/seurat/pbmc3k_tutorial.html to perform QC and various differential analyses using the Seurat package on ...
3
votes
2answers
596 views
Separate boxplots for multiple violin plot
I am using the following function from seurat package to generate multiple violon plots and I am interested in adding box plots to them but it doesn't work when I have plotted different data at once.
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4
votes
1answer
282 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
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2
votes
0answers
66 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
votes
1answer
73 views
Question about the dots on Quartile groups in boxplot
I have Microarray Normalized Expression data for a specific Gene. It looks like below in a dataframe B
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3
votes
2answers
310 views
Changing a wide range of colours to a limited gradient
I returned a FeaturePlot from Seurat to ggplot. My plot has a weird range of colours as below
I produced this plot by this code
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1
vote
0answers
105 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
vote
1answer
42 views
Error in annotating row names as data points in a PCA plot
I made a PCA plot and was trying to plot the eigenvenctors in R so that each data point is actually the sample name. All the samples are in column 1. The following are the R commands I am using:
<...
4
votes
1answer
112 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 ...
1
vote
0answers
77 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 ...
2
votes
2answers
655 views
Which data is being used for violin plot?
Sorry I just got totally confused conceptually.
If this is my raw count data
Likely, Seurat divides each value by sum of the column afterward times by 10000.
which gives so
...
3
votes
2answers
2k views
Mapping a list of cells in seurat featureplot
I have 209 cells, I clustered them by Seurat to 4 clusters. By Featureplot I am able to track a gene in clusters:
Higher color shows higher expression.
Now, for some genes I want to highlight some ...
2
votes
0answers
462 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 ...
4
votes
1answer
209 views
5
votes
1answer
2k views
FeaturePlot from Seurat: change its title
FeaturePlot is a function in Seurat package.
And in the vignette it is written that if we specify parameter do.return = TRUE it ...
0
votes
1answer
70 views
1
vote
1answer
159 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
...
2
votes
1answer
48 views
How can I find out the code DRIMSeq uses to make dmplotProportions objects?
I'm using DRIMSeq to do some analysis but I'd like to make my own figures from the results ideally using what they've done as a base.
I'm trying to find how they make their ggplot objects in the ...
