adjusting parameters in ViolinPlot did not work
Dear All,
I am using stack violin plot to visualize expression of genes in my single cell, but having hard time modifying the angle (circle in red, I would like to have it straight) and size of the markers in the plot (circle in blue, I would like to reduce the font size). Anyone could have a look at my script. I have tried to adjust all these parameters, but none of them work.
features <- c("CD3E","CD3D", "CD4", "CD8A", "FOXP3", "CCR7", "CD69", "CXCR3", "CXCR5", "CXCR6", "CCR4", "CCR6", "KLRB1", "IL2RA", "IL7R", "KLRG1", "CXCL13", "TOX", "LAG3", "CTLA4", "PDCD1", "HAVCR2", "TIGIT", "EOMES", "CX3CR1", "MKI67", "TRGV9",
"TRGV2", "FCGR3A", "NCAM1")
#plot
VlnPlot(all.annotated.subsets, features = features, stack = TRUE, flip = TRUE, adjust = 0.5) &
theme(legend.position = "none",
axis.text.x = element_text(size = 8, angle = 90),
axis.title = element_blank(),
axis.text.y = element_text(angle = 90, hjust = 1),
strip.text.y.left = element_text(angle = 90)) +
RotatedAxis()
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Ram
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synat.keam •
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synat.keam •
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written by synat.keam •
VlnPlot()produces a ggplot object, correct? Use+, not&to add your layers.Hi Ram, thank for your response!
+or&did not work at all"did not work at all" is insufficient feedback. Did you experiment with it, making sure the
+ ...was affecting the output at all or did you just replace the&with+, run the code and not see any change?VlnPlot()with multiple features will produce patchworked ggplot object - meaning there are multiple plots in a single returned visualization. Adding additional layers with the + as previously mentioned will only modify the last plot in the series of plots.You could try:
VlnPlot(..., combine = FALSE )Alternatively, if I were you, I'd
ggsave()the plot as a pdf or svg and just manually edit the plot. It would take < 1 min.Reproducibility is key and when the function is giving you a ggplot object, manipulating it manually is just a bad approach.
Adjusting the orientation of an axis label has no effect on reproducibility. I don't think your comment adds to the discussion.
I've edited my comment and removed the irrelevant part. If OP were to change parameters and generate a slightly different plot, they'd have to manually do the edits again. Plotting is usually an iterative process and I think as long as an automatable way exists to make the required change, using a manual tool to do it is just an unnecessary burden.