frequency_plot: Boxplot or Violin plot the count of cells expressing a...

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

Boxplot or Violin plot the count of cells expressing a certain marker

Usage

frequency_plot(
  x_df,
  gene,
  group.by = "condition",
  rep.by = "series",
  plot_type = "box",
  express_thres = 15,
  perc = T,
  add_pval = NULL,
  control_group = "base",
  AP = NULL,
  sum_table = F
)

Arguments

x_df	a dataframe
gene	which gene to plot
group.by	the experimental conditions
rep.by	the replication for each condition
express_thres	the fluorescence value by which a cell is called positive for a gene
perc	whether to show the percentage of positive cells or the number of positive cells
add_pval	which comparison groups in group.by to compare with control_group. If it is 'all', all pairs will be compared
box_plot	whether to use boxplot or violin plot

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.