Question: how to produce plots like this in R
1
gravatar for Javad
11 months ago by
Javad60
Javad60 wrote:

Dear all,

I am looking for the R package that I can use to produce this type of graphs:

download

I know ggplot2 has probably this capability but I can not find a proper tutorial to do it. I would be grateful if somebody can introduce a tutorial of how to produce these types of graphs.

Thanks

rna-seq • 1.5k views
ADD COMMENTlink modified 4 months ago by gaelgarcia05190 • written 11 months ago by Javad60

That appears more as a bubble plot rather a dot plot. If you indeed need a dot plot, try this

ADD REPLYlink written 11 months ago by Vijay Lakhujani4.1k

@OP: it would help if you posted some example data.

ADD REPLYlink written 11 months ago by cpad011211k
2
gravatar for jbalberge
11 months ago by
jbalberge80
France/Nantes
jbalberge80 wrote:

Assuming you're analyzing single-cell RNA seq data, you can use the DotPlot function from Seurat:

DotPlot(object = pbmc, genes.plot = features.plot, plot.legend = TRUE)

thanks to https://satijalab.org/seurat/visualization_vignette.html

ADD COMMENTlink written 11 months ago by jbalberge80

Sorry, but here should I normalise for number of cells in each group? I mean when the bigger circle shows higher number of cells

ADD REPLYlink written 11 months ago by Za120
1
gravatar for EagleEye
11 months ago by
EagleEye6.4k
Sweden
EagleEye6.4k wrote:

Try ggplot2 bubble chart

ADD COMMENTlink written 11 months ago by EagleEye6.4k
1

or this: https://ggplot2.tidyverse.org/reference/geom_dotplot.html ?

ADD REPLYlink written 11 months ago by cpad011211k
1
gravatar for cpad0112
11 months ago by
cpad011211k
India
cpad011211k wrote:

Please refer to dotplot function in clusterprofiler package: Look at Visualization of profile comparison section in https://bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

screenshot from the webpage:

bubblechart

ADD COMMENTlink modified 11 months ago • written 11 months ago by cpad011211k

Thanks a lot. It is a very good suggestion but the problem is that I need something that I have full control on the graph production. I need to factor the data and compare different data sets in a same figure. That is why I asked for a ggplot2 tutorial.

ADD REPLYlink written 11 months ago by Javad60
2

oh okay. Then probably, geom_dotplot function in ggplot might help you in plotting.

ADD REPLYlink written 11 months ago by cpad011211k
0
gravatar for gaelgarcia05
4 months ago by
gaelgarcia05190
UK
gaelgarcia05190 wrote:

This is from the Seurat DotPlot function, which is documented here:

https://github.com/satijalab/seurat/blob/master/R/plotting.R

Essentially, it is a ggplot geom_point plot.

ADD COMMENTlink written 4 months ago by gaelgarcia05190
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