Plot Median Percent Mito per Cell per Sample — Plot_Median_Mito (original) (raw)

Plot of median percent mito per cell per sample grouped by desired meta data variable.

Plot_Median_Mito(
  seurat_object,
  sample_col = "orig.ident",
  group_by = NULL,
  colors_use = NULL,
  dot_size = 1,
  plot_title = "Median % Mito per Sample",
  y_axis_label = "Percent Mitochondrial Reads",
  x_axis_label = NULL,
  legend_title = NULL,
  x_lab_rotate = TRUE,
  color_seed = 123
)

Arguments

seurat_object

Seurat object name.

sample_col

Specify which column in meta.data specifies sample ID (i.e. orig.ident).

group_by

Column in meta.data slot to group results by (i.e. "Treatment").

colors_use

List of colors or color palette to use. Only applicable if group_by is not NULL.

dot_size

size of the dots plotted if group_by is not NULL. Default is 1.

plot_title

Plot title.

y_axis_label

Label for y axis.

x_axis_label

Label for x axis.

legend_title

Label for plot legend.

x_lab_rotate

logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.

color_seed

random seed for the "varibow" palette shuffle if colors_use = NULL and number of groups plotted is greater than 36. Default = 123.

Examples

if (FALSE) {
# Add mito
obj <- Add_Mito_Ribo_Seurat(seurat_object = obj, species = "human")

# Plot
Plot_Median_Mito(seurat_object = obj, sample_col = "orig.ident",  group_by = "sample_id")
}