volcano3D (version 2.0.9)

forest_plot: Forest plot individual gene from 2x3 factor analysis

Description

Forest plot individual gene from 2x3 factor analysis using either base graphics, plotly or ggplot2.

Usage

forest_plot(
  object,
  genes,
  scheme = c("red", "green3", "blue"),
  labs = NULL,
  error_type = c("ci", "se"),
  error_width = 0.05,
  gap = 1,
  transpose = FALSE,
  mar = if (transpose) c(5, 7, 5, 4) else c(5, 5, 5, 3),
  ...
)
forest_plotly(
  object,
  genes,
  scheme = c("red", "green3", "blue"),
  labs = NULL,
  error_type = c("ci", "se"),
  error_width = 4,
  gap = 1,
  transpose = FALSE,
  ...
)
forest_ggplot(
  object,
  genes,
  scheme = c("red", "green3", "blue"),
  labs = NULL,
  error_type = c("ci", "se"),
  error_width = 0.3,
  facet = TRUE,
  gap = 1,
  transpose = FALSE,
  ...
)

Value

Returns a plot using either base graphics (forest_plot), plotly (forest_plotly) or ggplot2 (forest_ggplot). forest_plot also invisibly returns the dataframe used for plotting.

Arguments

object

A 'volc3d' class object from a 2x3 analysis generated by deseq_2x3_polar()

genes

Vector of genes to plot

scheme

Vector of 3 colours for plotting

labs

Optional character vector of labels for the groups

error_type

Either "ci" or "se" to specify whether error bars use 95% confidence intervals or standard error

error_width

Width of error bars

gap

Size of gap between groupings for each gene

transpose

Logical whether to transpose the plot

mar

Vector of margins on four sides. See par()

...

Optional arguments

facet

Logical whether to use facets for individual genes (ggplot2 only)

See Also

deseq_2x3_polar()