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
82
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stacked barplot with error bars
I need to create a barplot with error bars, my data consists of 2 groups called "Genot", with 3 sub-groups "Suberin" for each, associated with a value "Percent".
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1
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Intepreting and applying ordinal logistic regression coefficients to calculate probabilities?
Can someone help hint me how I can interpret ordinal logistic regression coefficients and how I can use the .L, .Q and .C terms to calculate probabilities? I am analysing a dataset, where people ...
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Plot error and blank tab of plot
I am trying to plot by using these commands , but this is the error I am getting, and I tried multiple times, even by making the window size larger, the [lot tab is empty/blank too.
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Removing missing categories from geom_bar
I have a simple dataframe that includes points where the x values are 0, 1, 2, 3, 4, and 7. When I go to plot the data this is what ggplot2 gives me:
I only want to include the points mentioned above....
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change the order in ggplot
I'm trying to make a plot that looks like this:
This is a rudimentary plot I did in excel. It's a plot of reads by length. Very simple nothing crazy to it. The important thing to note is that it's ...
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107
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Histogram plot using R/python with two variables[BC and Control] and their corresponding gene names
How do we plot histogram in R\Python with two variables[BC and Control] and their corresponding gene names examples is below:
Thank you,
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1
answer
613
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How to change the position of groups colors in DimPlot of Seurat
I have a Seurat object and plotted the Dimplot for UMAP visualization for 2 variables, as shown in the image below.
Now, the problem is that I want the group by variables such as ...
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2
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111
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Display row and column names in R
I have plotted a heat-map with 235 rows and 570 columns which is below: how do we make clear names of row and columns on this graph using R?
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297
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Expending UpsetR plot with Orthofinder families and gene numbers
I can create an Upset plot with the input file, which can be found here
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1
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140
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Manually order the set fails in UpsetR
This question was also asked on Biostars
I have tried to use UpsetR to visualise the input file, which can be found here. How is it possible to make UpsetR accept an order defined in ...
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1
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96
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Can I run dotPlotly from Rstudio?
I'd like to run dotPlotly from RStudio but I can't find any description/help for this. Is it at all possible?
Another side to this question: does anyone know any tool for dot plots for genome ...
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1
answer
169
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How to make bar bigger in UpsetR plot
I have tried to use UpsetR to visualize the input file which can be found here.
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1
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275
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replacement has 1 row, data has 0
I have tried to use UpsetR to visualize the input file which can be found here
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127
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Create VIP plot using R from the SIMCA VIP values
I am using SIMCA software to perform multivariate analysis and want a VIP scores plot in R as shown below.
which package is used for this type of plot (image retrieved from Google-images)??
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1
answer
90
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How to plot stacked bar chart using R showing mean with range and labelled values?
I am trying to plot a stacked bar graph with mean values from multiple repeats, also showing the range of the data and values labelled.
My data frame is below:
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2
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1k
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How to remove black outline from Seurat's VlnPlot violin plot
Using Seurat's VlnPlot, how can I remove the black outline around the violin plot?
For example, how can I change from the following graph with a (black) outline:
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262
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How to make a violin plot around quasirandom dots
I want to have a plot violin plot around quasirandom dots - like below
This is my data
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1
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72
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Jitter violin coloured by sample id
I want to have a jitter violin coloured by sample ids but I get this weird plot
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1
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60
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ggtree：How to keep leading zero ‘0’ in the tiplabel？
I am using ggtree to draw a phylogenetic tree.
Some taxa IDs have a 0 at the beginning.
However, when I plot the tiplabel the leading zero is automatically dropped. ...
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1
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512
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Violin plots appear as vertical lines
I want to perform a violin plot from a Seurat object and I rather have vertical lines. How can I stop this and rather have a standard Violin plot?
code
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1
answer
1k
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Grouping x-axis in scatter plot
I am trying to plot one scatter plot for each group, where each group has continous values in x-axis.
Reference Data
Gives continuous x-axis but all groups are combined.
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0
answers
86
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Pulling out genes in a scatterplot
I'm comparing gene expression among 2 different datasets (in vivo and in vitro) I have made a heatmap showing the correlation for each and then plotted the data frame to create a scatterplot. Now I ...
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86
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2
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92
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Arrange ggplot Figure for scRNA-seq data
I have generated a ggplot for 8 single-cell libraries, with the purpose of visualizing the tSNE facet plot by sample, colored by cell type -- with percentages. The best I could get to is this -
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27
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Calculating percent mouse cells per sample
I want to see the correlation between % mouse reads per sample vs % mouse cells per sample. I've already calculated the % mouse reads per sample but I'm stuck on calculating the % of mouse cells per ...
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2
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1k
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ViolinPlot x-axis
I'm trying to set the x-axis in my Violin Plot to go by each patient rather than it being scattered.
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95
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How to plot the gap distribution of contigs wrt to reference genome
I have a contigs file that I generated using Minia and then I have used Minimap2 to map these contigs again to the reference genome. Now I want to plot the gap distribution i.e. gap distance of the ...
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481
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Barplot without alphabetizing x-axis
I'm inputting a .csv file and then plotting a barplot based on the colnames but when I go plot the order the names are being alphabetized rather than get the order that is in the .csv file. How to I ...
- 371
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2
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3k
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PCA plot in R coloured by sample type
I'm a biologist, not a programmer so please be gentle.
So I have a dataset that looks like
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1
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119
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Multiple box plot
I am using below code to plot multiple box plot but I am still struggling to understand how I can add whisker to box plot and how to change sample order like in this figure SampleType?
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0
answers
62
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How to call this : some dots in volcano plot aligned a line after add a very small value to padj
when I plotting the volcano plot, I got some dots very top of the Y-axis because their padj nearly reached 0（I checked the data, I think they are reliable）, so I followed the advice to add a very ...
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1
answer
723
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ggplot2 geom_bar() , do not merge y-values shared same x-ids [closed]
I am plotting a barplot using ggplot + geom_bar() function in R.
I have some the recoreds which share the same x-axis ...
- 81
2
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1
answer
350
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Plot information stored in dataframe within a tree (ggtree)
Hello to the entire Stackoverflow community!
I'm writing to you because I'm currently building a phylogeny with ggtree and I have in parallel a table like this one:
df :
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83
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1
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980
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2
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97
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Grouping a set of genes in a ggplot object
I have a boolean matrix of mutated or non mutated genes across some samples
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1
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65
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How to visualise the proportion of clonal genes to sub clonal genes [duplicate]
I have a data frame
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-4
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1
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75
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1
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1
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54
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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 ...
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80
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163
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89
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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 ...
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1
answer
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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 ...
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2
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1k
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Making a volcano plot look less cluttered
I have generated a volcano plot with a differential expression file.
Code for inputing file:
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1
answer
157
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Bar plot with error bars
I am trying to plot a box plot/stacked bar graph with error bars.
output of dput(DF)
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- 371
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1
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59
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Dodged bar chart
I want to create a dodged barchart with different cell cycles for each cell type within each condition.
dput(DF_count)
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- 371
2
votes
1
answer
3k
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Pulling out a certain gene in a volcano plot
I have generated a volcano plot with a differential expression file.
Code for inputing file:
...
- 371
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votes
1
answer
8k
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stacked bargraph with error bars
I'm attempting to plot a stacked barplot with ggplot2 with this code:
...
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2
answers
513
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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 ...
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0
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1
answer
559
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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 ...
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