plot_gene_set_mean: Plot the Mean Gene Expression Profiles with Optional Standard...

In drostlab/myTAI: Evolutionary Transcriptomics

Plot the Mean Gene Expression Profiles with Optional Standard Deviation and Labels

Description

This function visualizes the mean gene expression profiles for the stages defined in the input ExpressionSet. It can also display the standard deviation as a shaded area around the mean, add labels with the expression values at each stage, and customize various plot parameters.

Usage

plot_gene_set_mean(
  ExpressionSet,
  y_ticks = 6,
  digits = 2,
  color = "#009999",
  line_width = 2,
  point_size = 3,
  add_values = T,
  xlab = "Ontogeny",
  ylab = "Mean Expression Level",
  add_sd = F,
  yaxis_range = 4,
  shadow_color = "grey"
)

Arguments

ExpressionSet	a standard PhyloExpressionSet or DivergenceExpressionSet object containing gene expression data.
y_ticks	a numeric value specifying the number of ticks to be drawn on the y-axis. Default is 6.
digits	a numeric value specifying the number of digits to display in the expression value labels. Default is 2.
color	a string specifying the color of the line and points representing the mean expression. Default is "#009999".
line_width	a numeric value specifying the line width for the mean expression line. Default is 2.
point_size	a numeric value specifying the size of the points representing the mean expression values. Default is 3.
add_values	a logical value indicating whether expression values should be displayed on the plot. Default is TRUE.
xlab	a string specifying the label for the x-axis. Default is "Ontogeny".
ylab	a string specifying the label for the y-axis. Default is "Mean Expression Level".
add_sd	a logical value indicating whether the standard deviation should be shown as a shaded ribbon around the mean expression. Default is FALSE.
yaxis_range	a numeric value specifying the extra range added to the y-axis when standard deviation is shown. Default is 4.
shadow_color	a string specifying the color of the shaded area representing the standard deviation. Default is "grey".

Author(s)

Filipa Martins Costa

Examples

#In case you want the expression values show together with the standard deviation
plot_gene_set_mean(ExpressionSet = PhyloExpressionSetExample,
                  add_sd = TRUE)
                  
#In case you would like for the expression values and the standard deviation don't show up
plot_gene_set_mean(ExpressionSet = PhyloExpressionSetExample,
                  add_values = FALSE)

drostlab/myTAI documentation built on June 13, 2025, 6:24 a.m.