plot_emb_circle_scale() output low resolutation image

[zhenzuo2]

Hi,

My data has about 100, 000 cells and the figure generated by plot_emb_circle_scale() is of poor image quality (huge pixels).

png(some_output_path,
    units = "in", width = 15, height = 15, res = 600)
p <- plot_emb_circle_scale(sce, dimred = "UMAP", point.size = 0.5, point.alpha = 1) +
  theme_bw(base_size = 14)
legend <- circle_scale_legend(text.size = 5, alpha = 0.9)
plot_grid(p, legend, ncol = 2, rel_widths = c(1, 0.4))
dev.off()

I am not sure if it is caused by large sample size or default raster() argument. I can attach output image if needed.

[zhenzuo2]

[sjczheng]

Could you make a pdf file to see how it looks?

[sjczheng]

And have you tried changing your res values in the png function?

[zhenzuo2]

pdf(path_to_save,
    width = 15, height = 15)
p <- plot_emb_circle_scale(sce, dimred = "UMAP", point.size = 0.5, point.alpha = 1) +
  theme_bw(base_size 
legend <- circle_scale_legend(text.size = 5, alpha = 0.9)
plot_grid(p, legend, ncol = 2, rel_wi
dths = c(1, 0.4))
dev.off()

It does not work. I also tried ggsave(). But none of them worked.

[zhenzuo2]

And have you tried changing your res values in the png function?

res = 600 is pretty high. It usually generated 20M figures. But the png saved by plot_emb_circle_scale() is less than 1M.

[sjczheng]

Yes. You are right. The size of the figure is much smaller than a regular ggplot scatter plot. The reason is that I use scatter more package (https://github.com/exaexa/scattermore) to plot the points. It seems like a rater issue by scattermore package. Could you change the point.size to 1 in plot_emb_circle_scale function to test? I kind of remember there is an issue if you use point.size less than 1 in scattermore.

[zhenzuo2]

[zhenzuo2]

Thank you. scattermore is much faster than a regular ggplot scatter plot. Rasterization may be a problem when raster size is too large.

[sjczheng]

Yeah. You may need to paly a little with the figure size to make it work. It seems to me that your figure size is too big.

[kasperdanielhansen]

Worth sending a report to scattermore authors

Best, Kasper (Sent from my phone.)

On Nov 2, 2021, at 15:37, Shijie C. Zheng @.***> wrote:

 Closed #3.

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