Change the y limits ( especially the minimum) with Vlnplot

The VlnPlot function in the Seurat R package uses ggplot2 to draw the violin plot. This means we can modify the y-axis using scale_y_continuous.

In your case, to change the y-axis of your violin plot to 3000-10000, we would write:

VlnPlot(object, features, cols = NULL, pt.size = 0.1) + scale_y_continuous(limits = c(3000,10000))

To show you a reproducible example, we can draw a violin plot using the pbmc_small dataset from the Seurat package:

VlnPlot(pbmc_small, "CD3E")

default violin plot

The plot above has a default axis of 0 to around 6.3. Here is how the same plot looks like after altering the y-axis using scale_y_continuous, in which I zoom in between 0 and 3:

VlnPlot(pbmc_small, "CD3E") + scale_y_continuous(limits = c(0,3))

violin plot after changing axis

Many of the other visualizations in the Seurat package also use ggplot2, so you can make all types of cosmetic changes to them using various ggplot2 commands (themes, axis labels, colors, etc.)