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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Expending UpsetR plot with Orthofinder families and gene numbers

I can create an Upset plot with the input file, which can be found here ...
user3523406's user avatar
2 votes
0 answers
86 views

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 ...
mmpp's user avatar
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2 votes
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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 ...
mmpp's user avatar
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2 votes
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192 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 ...
kcm's user avatar
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1 vote
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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)??
Najeha Mohamed's user avatar
1 vote
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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 ...
Chu's user avatar
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1 vote
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261 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 ...
Jerry07's user avatar
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1 vote
0 answers
647 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: ...
Gurkamal Deol's user avatar
1 vote
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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 ...
Zizogolu's user avatar
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0 votes
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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. ...
Samia's user avatar
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-1 votes
1 answer
139 views

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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