Question: how to produce plots like this in R
3
gravatar for Javad
22 months ago by
Javad90
Javad90 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 • 3.6k views
ADD COMMENTlink modified 16 months ago by gaelgarcia05210 • written 22 months ago by Javad90

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

ADD REPLYlink written 22 months ago by lakhujanivijay5.0k

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

ADD REPLYlink written 22 months ago by cpad011213k
3
gravatar for jbalberge
22 months ago by
jbalberge130
France/Nantes
jbalberge130 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 22 months ago by jbalberge130

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 22 months ago by Za120
2
gravatar for cpad0112
22 months ago by
cpad011213k
India
cpad011213k 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 22 months ago • written 22 months ago by cpad011213k

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 22 months ago by Javad90
2

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

ADD REPLYlink written 22 months ago by cpad011213k
1
gravatar for EagleEye
22 months ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

Try ggplot2 bubble chart

ADD COMMENTlink written 22 months ago by EagleEye6.6k
1

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

ADD REPLYlink written 22 months ago by cpad011213k
0
gravatar for gaelgarcia05
16 months ago by
gaelgarcia05210
UK
gaelgarcia05210 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 16 months ago by gaelgarcia05210
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