Single Cell RNA-Seq Analysis in R With Seurat|scRNA-seq Analysis Seurat|Bioinformatics for beginners

[@lucreziamatilde8728]

Thanks Mr bioinformatiX 😊

[@MrBioinformatiX]

Thank you, you're welcome 😊

[@traveller_of_lyf]

Thank you so much 🙏 for this video. Also, when plotting violin plot of ny dataset I got only black dots orange thing was missing. How to resolve this error?

[@MrBioinformatiX]

Thank you for your kind words 😊 The issue of seeing only black dots without the violin shapes in a `VlnPlot` during single-cell RNA-seq analysis can arise from various factors. One common reason is a small sample size; if the dataset has very few cells, the violin shapes may not render, leaving only individual data points visible. Another possibility is incorrect feature specification, where the features passed to the `features` parameter (e.g., `nCount_RNA`, `percent.mt`) are not present in the dataset. You should verify this by inspecting the metadata with `head(pbmc[[]])`. Default plotting parameters in Seurat, such as `pt.size` or `adjust`, can also affect how violins are displayed; explicitly setting these parameters (e.g., `pt.size = 0.1, adjust = 1`) often resolves the issue. Additionally, differences in library versions, particularly Seurat or ggplot2, may lead to inconsistent rendering, so ensuring these packages are up-to-date is crucial. I hope it works with you 😊

[@traveller_of_lyf]

@MrBioinformatiX thank you so much for your explanation.

[@MrBioinformatiX]

@@traveller_of_lyf No worries 😊

[@LailaFarouk-e7p]

Thanks

[@MrBioinformatiX]

You're welcome