Create a volcano plot to compare molecule counts between 2 conditions.

Create a boxplot/jitter plot to show molecule counts distribution.

cmp_volcano(
  object,
  y_axis = c("p_values", "padj"),
  x_lim = c(-2.5, 2.5),
  colors = rev(RColorBrewer::brewer.pal(7, "Spectral")),
  text_y_lim = 100,
  text_x_lim = 1,
  text_size = 4,
  title = NULL,
  max.overlaps = 10
)

Arguments

object

A STCompR object.

y_axis

Character vector specifying the y-axis variable. Options are "p_values" or "padj".

x_lim

Numeric vector specifying the x-axis limits. Default is c(-2.5, 2.5).

colors

Color palette for the plot. Default is RColorBrewer::brewer.pal(7, "Spectral").

text_y_lim

Numeric value specifying the threshold for feature labels on the y-axis. Genes with -log10(p-value) less than this threshold will not be labeled. Default is 100.

text_x_lim

Numeric value specifying the threshold for feature labels on the x-axis. Genes with absolute x-values less than this threshold will not be labeled. Default is 2.

text_size

Numeric value specifying the size of text labels in the plot. Default is 5.

title

A title for the diagram.

max.overlaps

The maximum number of label overlaps.

Examples

example_dataset("11284296/files/cmp_xen")
#> |-- INFO :  Dataset 11284296/files/cmp_xen was already loaded. 
cmp_xen
#> |-- INFO :  An object of class STCompR 
#> |-- INFO :  xen_r1 Condition_1 
#> |-- INFO :  xen_r2 Condition_2 
#> |-- INFO :  Number of features:  7 
#> |-- INFO :  >>> Please, use show_st_methods(class = 'STCompR') to show availables methods <<< 
cmp_volcano(cmp_xen)