violinPlot_mod.Rd
Create violin plot of gene expression data across groups
violinPlot_mod(
object,
assay,
slot,
genes,
group,
facet_by = "",
filter_outliers = F,
outlier_low = 0.05,
outlier_high = 0.95,
jitter_points,
jitter_dot_size
)
Seurat-class object
Assay to extract gene expression data from (Default: SCT)
Slot to extract gene expression data from (Default: scale.data)
Split violin plot based on metadata group
Include only a specific subset from group.by
Genes to visualize on the violin plot
Filter outliers from the data (TRUE/FALSE)
Scale data from 0 to 1 (TRUE/FALSE)
Transform data onto a log10 scale (TRUE/FALSE)
Numeric data will be ordered naturally by default. Toggling this option will order the groups to match the group list if non-numeric, and will have no effect if otherwise.
Give alternative names to group.by displayed on the graph
Y-axis limit
Choose between grid, labeled, and row
Filter lower bound outliers (Default = 0.1)
Filter upper bound outliers (Default = 0.9)
Scatter points on the plot (TRUE/FALSE)
Set spread of jittered points
Set size of individual points
Print outliers as points in your graph that may be redundant to jitter
violin ggplot2 object
Takes in a list of genes inputted by the user, displays violin plots of genes across groups from a slot-assay with (optional) outliers removed. Can also choose to scale or transform expression data.