PlotPDF resolution

[ankushs0128]

I would like to generate a high-resolution figure. Using the Plot PDF function, The zoomed-in figures especially UMAP are pixelated. Screenshot enclosed

plot(p2, name = "_1_Plot-UMAP1-Clusters.pdf", ArchRProj = Differentiation_P_1, addDOC = TRUE, width = 
20, height = 20,plotList = NULL)

How can I improve the figure plotting resolution in ARCHR for all figures?
Thanks

[rcorces]

Please note that I have converted this issue into a discussion topic because issue reports are only meant for problems with the software. All questions and feature requests should be reported in the discussions area. This is stated in the issue request screen and in the issue template.

To answer your question, plotPDF() is only meant to take already generated plots and print them onto a PDF. For the most part, plotPDF() has nothing to do with the resolution.

In your particular example, I'm assuming that this is an embedding plot that was created using plotEmbedding(). If you look at the parameters for plotEmbedding() you will see rastr as well as .... When rastr = TRUE you convert vector graphics into rasterized graphics and this results in the blurred dots that you mention. If you use rastr = FALSE each point will be stored as an individual vector at absolute resolution. However, editing files with tens of thousands of individual vectorize points is challenging for most graphics cards. So you can set rastr = FALSE and have perfect resolution.

Alternatively, you can look into the ... which allows you to pass additional parameters to ArchR::ggPoint() or also directly to ggPlot

[ankushs0128]

Apologies and Thanks

[sneddonucsf]

Hi @rcorces to piggy back off of this, how can we plot a vectorized plot for the "plotMarkers" function? I see that it does not have a "rastr = FALSE" option, nor the "..."

[rcorces]

@sneddonucsf - there was not previously an option to return this plot without rasterization. I believe this is because the number of points is very large and this could be problematic for certain environments. I've added the option via ee6bc0b on the dev_plotMarkers branch which comes off of release_1.0.2. The default is still to rasterize for safety.

You can test this out by installing this new branch, restarting your R session, and reloading ArchR

devtools::install_github("GreenleafLab/ArchR", ref="dev_plotMarkers", repos = BiocManager::repositories())

Please let me know if this works for you as I have not tested this.

[sneddonucsf]

Seems to have worked, thank you!