Low quality images

[PietroAnc]

Hi, i'm trying to plot the UMAP of cell cycle phases using the plot_emb_circle_scale function. However, the plot seems really blurry with a bad quality. Can't find a way to improve it. I converted my Seurat object into a SCE one, so my UMAPs produced with Seurat are really HQ compared to cell cycle one. Is there something i am missing?

here's the code

plot_emb_circle_scale(
sce,
color_by = "tricyclePosition",
facet_by = NULL,
dimred = "umap.cca",
dim = seq_len(2),
fig.title = NULL,
point.size = 1.2,
point.alpha = 0.6,
x_lab = "UMAP1",
y_lab = "UMAP2",
hue.colors = c("#2E22EA", "#9E3DFB", "#F86BE2", "#FCCE7B", "#C4E416", "#4BBA0F",
"#447D87", "#2C24E9"),
hue.n = 1000,
plot.legend = FALSE
)

And here's the image. There's no improvement in downloading it as pdf, still blurry.

Thanks in advance!

[kasperdanielhansen]

My guess is that this has to do with the device you're plotting to. How are you rendering the PNG? How are you saving it? Best, Kasper

…

On Thu, Mar 20, 2025 at 2:30 PM PietroAnc ***@***.***> wrote: Hi, i'm trying to plot the UMAP of cell cycle phases using the plot_emb_circle_scale function. However, the plot seems really blurry with a bad quality. Can't find a way to improve it. I converted my Seurat object into a SCE one, so my UMAPs produced with Seurat are really HQ compared to cell cycle one. Is there something i am missing? here's the code plot_emb_circle_scale( sce, color_by = "tricyclePosition", facet_by = NULL, dimred = "umap.cca", dim = seq_len(2), fig.title = NULL, point.size = 1.2, point.alpha = 0.6, x_lab = "UMAP1", y_lab = "UMAP2", hue.colors = c("#2E22EA", "#9E3DFB", "#F86BE2", "#FCCE7B", "#C4E416", "#4BBA0F", "#447D87", "#2C24E9"), hue.n = 1000, plot.legend = FALSE ) And here's the image. There's no change in downloading it as pdf, still blurry. Thanks in advance! image.png (view on web) <https://github.com/user-attachments/assets/c2e0db97-eb94-4b2c-b1d0-ae0b6d137709> — Reply to this email directly, view it on GitHub <#22>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABF2DH55SC2TGIPHOGEZTZD2VLGGVAVCNFSM6AAAAABZNTMPU6VHI2DSMVQWIX3LMV43ASLTON2WKOZSHEZTKNRZGQ4TSMQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [image: PietroAnc]*PietroAnc* created an issue (hansenlab/tricycle#22) <#22> Hi, i'm trying to plot the UMAP of cell cycle phases using the plot_emb_circle_scale function. However, the plot seems really blurry with a bad quality. Can't find a way to improve it. I converted my Seurat object into a SCE one, so my UMAPs produced with Seurat are really HQ compared to cell cycle one. Is there something i am missing? here's the code plot_emb_circle_scale( sce, color_by = "tricyclePosition", facet_by = NULL, dimred = "umap.cca", dim = seq_len(2), fig.title = NULL, point.size = 1.2, point.alpha = 0.6, x_lab = "UMAP1", y_lab = "UMAP2", hue.colors = c("#2E22EA", "#9E3DFB", "#F86BE2", "#FCCE7B", "#C4E416", "#4BBA0F", "#447D87", "#2C24E9"), hue.n = 1000, plot.legend = FALSE ) And here's the image. There's no change in downloading it as pdf, still blurry. Thanks in advance! image.png (view on web) <https://github.com/user-attachments/assets/c2e0db97-eb94-4b2c-b1d0-ae0b6d137709> — Reply to this email directly, view it on GitHub <#22>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABF2DH55SC2TGIPHOGEZTZD2VLGGVAVCNFSM6AAAAABZNTMPU6VHI2DSMVQWIX3LMV43ASLTON2WKOZSHEZTKNRZGQ4TSMQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Best, Kasper

[PietroAnc]

Thanks for the prompt respond Kasper,

The problem is that even when in the "Plots" section of R console the plot looks blurry. If I plot an UMAP with

FeaturePlot(...etc), it looks fine. Also the circle_scale_legends looks fine. The problem is just the UMAP projection of cell cycle.

Best,
Pietro

[CroixJeremy2]

I have the same problem, but I made a workaround that enables more customisation. Here it is:

#Calculating the cell cycle score in [0; 2π] interval using tricycle package
	library(tricycle)

	#JoinLayers first
	MY_SEURAT = JoinLayers(MY_SEURAT)

	#Converting Seurat object to SingleCellExperiment object
	MY_SEURAT_SingleCellExperiment = as.SingleCellExperiment(x = MY_SEURAT)

	#Calculating
	MY_SEURAT_SingleCellExperiment = project_cycle_space(x = MY_SEURAT_SingleCellExperiment, gname.type = "SYMBOL", species = "mouse")
	MY_SEURAT_SingleCellExperiment = estimate_cycle_position(MY_SEURAT_SingleCellExperiment)
	# colData(MY_SEURAT_SingleCellExperiment)

	#Transfering scores to the original Seurat objet
	MY_SEURAT$tricyclePosition = MY_SEURAT_SingleCellExperiment$tricyclePosition

#Plot
	retreived_color_palette = colorRampPalette(c("#2E22EA", "#9E3DFB", "#F86BE2", "#FCCE7B", "#C4E416", "#4BBA0F", "#447D87", "#2C24E9")) #based on the source code of the tricycle package

	FeaturePlot_scCustom(seurat_object = MY_SEURAT, features = "tricyclePosition", pt.size = 1, na_cutoff = min(MY_SEURAT$tricyclePosition)) &
					scale_colour_gradientn(colours = retreived_color_palette(100), limits = c(0, 2*pi), breaks = c(0, 0.50*pi, pi, 1.50*pi, 2*pi), labels = c("0", "0.50π", "π", "1.50π", "2π"))

Tell me if it not reproducible or something else.
Best regards everybody,