Questions tagged [ggplot2]

Advanced R visualisation and plotting package based on the grammar of graphics. ggplot2 is also available in Python via 'plotnine' which uses ggplot2 code

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7
votes
1answer
94 views

Density plot, scale it to 0-1

Doubt regarding density plot what is the scale being plotted in the Y axis.Is it possible to scale it to 1?. This is my code ...
6
votes
1answer
3k 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 ...
4
votes
1answer
477 views

How to enlarge a section of y-axis?

I am using ggplot2 to plot a scatter plot. ...
4
votes
1answer
443 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 ...
4
votes
1answer
181 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 ...
3
votes
3answers
4k 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 ...
3
votes
2answers
568 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 ...
3
votes
1answer
839 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
2k 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. ...
3
votes
1answer
179 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
340 views

Pulling out a certain gene in a volcano plot

I have generated a volcano plot with a differential expression file. Code for inputing file: ...
2
votes
1answer
410 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
votes
2answers
1k 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 ...
2
votes
1answer
57 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 ...
2
votes
1answer
104 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 ...
2
votes
1answer
402 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: ...
2
votes
1answer
134 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 ...
2
votes
1answer
988 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 ...
2
votes
0answers
89 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
0answers
669 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
vote
1answer
174 views

Visualizing the difference among three groups

I have 3 data frames for three groups of patients 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 have ...
1
vote
1answer
45 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: <...
1
vote
1answer
262 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 ...
1
vote
1answer
245 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
67 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
vote
0answers
51 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
0answers
218 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
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
votes
1answer
229 views

Changing the legend names

...
0
votes
1answer
44 views

Griding ggplot object in r

I have this data frame head(d) ...
0
votes
1answer
413 views

Changing the axis limits of ggplot objects

By EnhancedVolcano R package I have this plot with this code ...
0
votes
1answer
34 views

Very low probability densities

I'm generating a density plot using the ggplot2 library: ...
0
votes
1answer
44 views

Getting weird plot with ggpubr package

I have a data frame for two groups and 9 variables ...
0
votes
2answers
75 views

Grouping a set of genes in a ggplot object

I have a boolean matrix of mutated or non mutated genes across some samples ...
0
votes
3answers
70 views

Boxplot of read length distributions from multiple samples

Newbie R user here. I want to create a plot with boxplots of read length distribution on the Y-axis, and samples on the X-axis -- like this image from doi: 10.1038/srep16498 However, I'm not sure ...
0
votes
1answer
58 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 ...
0
votes
1answer
40 views

A box plot of qualitative variables

I have 2 groups of patients; responders to chemotherapy and non-responders I have calculated cancer cell fraction (CCF) of a set of driver genes (by variant allele frequency) for each group and I ...
0
votes
2answers
191 views

Making a volcano plot look less cluttered

I have generated a volcano plot with a differential expression file. Code for inputing file: ...
0
votes
1answer
33 views

Dodged bar chart

I want to create a dodged barchart with different cell cycles for each cell type within each condition. dput(DF_count) ...
0
votes
1answer
281 views

stacked bargraph with error bars

I'm attempting to plot a stacked barplot with ggplot2 with this code: ...
0
votes
1answer
78 views

Stacked barplot for single cell analysis

I want to create a stacked bar-graph with different cell cycles for each cell type within each condition. I have uploaded the file for it. Don't know how to go about it as now I have another condition ...
0
votes
1answer
801 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: ...
0
votes
1answer
453 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 ...
0
votes
0answers
21 views

comparing two groups using R bar graph

I have two data frames. Let say TissueA and TissueB. I want to compare these two data frames by bar graph in R. ...
0
votes
2answers
46 views

Clustered column chart for single cell data

I want to create a column plot for my single cell analysis that has 2 sample types, a normal and PDAC. I want to show, the percentage of different cell types per sample type. How do I go about ...
0
votes
1answer
55 views

Bar plot with error bars

I am trying to plot a box plot/stacked bar graph with error bars. output of dput(DF) ...
0
votes
0answers
122 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
votes
0answers
44 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 ...
-1
votes
2answers
61 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 ...
-1
votes
1answer
75 views

Showing name of genes in boxplot

I have a long format data frame like this ...