Violin plot of spatially profiled genes — violinPlot • DSPWorkflow

Returns violin plot of user-input gene(s) expression across groups, can optionally subdivide groups into a more specific category

violinPlot(
  object,
  expr.type = "q_norm",
  genes = c("FOXP3", "CD4"),
  group = "CellType",
  facet.by = "none"
)

Arguments

object: Name of NanostringGeoMxSet to perform analysis on
expr.type: Name of normalized expression data slot
genes: Transcript(s) to be plotted on the y-axis of the violin plot
group: Metadata group to be plotted on the x axis of the violin plot
facet.by: Further subdivide group by this category (Default: NULL)

Value

an arranged grob of violin plots

Details

ggplot function that takes in gene expression data from NanostringGeoMxSet, outputs the distribution of gene expression values across groups. Requires normalized expression data and valid group category to be present in object