forest_plot function

Forest plot individual gene from 2x3 factor analysis

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

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,
  ...
)

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)

Returns

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.

See Also

deseq_2x3_polar()