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

Source: R/plot_gene_set_mean.R
plot_gene_set_mean.Rd

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

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)
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.

                  
#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)