View source: R/plot_gene_set_mean.R
plot_gene_set_mean | R Documentation |
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.
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"
)
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 |
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 |
xlab |
a string specifying the label for the x-axis. Default is |
ylab |
a string specifying the label for the y-axis. Default is |
add_sd |
a logical value indicating whether the standard deviation should be shown as a shaded ribbon around the mean expression. Default is |
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 |
Filipa Martins Costa
#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)
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