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Questions tagged [ggplot2]

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

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21 views

Seurat VlnPlot presenting expression of multiple genes in a single cluster

Seurat VlnPlots are most commonly used to visualize differences in any given gene expression across multiple clusters or cell types. For example: ...
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0answers
23 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 ...
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1answer
42 views

How do I increase the minimum dot size in Seurat's DotPlot function?

I want to use the DotPlot function from Seurat v3 to visualise the expression of some genes across clusters. However when the expression of a gene is zero or very low, the dot size is so small that it ...
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1answer
21 views

Customizing colors in geom_arc_bar (ggforce)

I am trying to plot scatter plot of pie charts using ggplot2 and ggforce. Following is my code ...
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1answer
87 views

Changing the axis limits of ggplot objects

By EnhancedVolcano R package I have this plot with this code ...
2
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1answer
56 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 ...
2
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1answer
102 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
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1answer
119 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
42 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
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1answer
446 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 ...
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0answers
39 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
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1answer
181 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: ...
3
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1answer
157 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
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1answer
493 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
707 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. ...
4
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1answer
300 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 ...
2
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0answers
68 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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1answer
80 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 ...
3
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2answers
322 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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0answers
114 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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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
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1answer
118 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
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0answers
78 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
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2answers
719 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
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2answers
3k 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
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0answers
488 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
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1answer
229 views

How to enlarge a section of y-axis?

I am using ggplot2 to plot a scatter plot. ...
5
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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
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1answer
77 views

Changing the legend names

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1
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1answer
178 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
51 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 ...