Plot the Expression Profiles of a Gene Set

This function simply visualizes the gene expression profiles of a defined subset of genes stored in the input ExpressionSet. The maximum nummber of genes to visualize at once is 25.

Usage

plot_gene_set(
  ExpressionSet,
  gene_set,
  get_subset = FALSE,
  use_only_map = FALSE,
  colors = NULL,
  plot_legend = TRUE,
  y_ticks = 6,
  digits_ylab = 1,
  line_width = 1,
  point_size = 2,
  add_expression_values = FALSE,
  n_genes_for_distance = 1,
  ...
)

Arguments

ExpressionSet: a standard PhyloExpressionSet or DivergenceExpressionSet object.
gene_set: a character vector storing the gene ids for which gene expression profiles shall be visualized.
get_subset: a logical value indicating whether or not an ExpressionSet subset of the selected gene_set should be retuned.
use_only_map: a logical value indicating whether instead of a standard ExpressionSet only a Phylostratigraphic Map or Divergene Map is passed to the function.
colors: colors for gene expression profiles. Default: colors = NULL, hence default colours are used.
plot_legend: a logical value indicating whether gene ids should be printed as legend next to the plot.
y_ticks: a numeric value specifying the number of ticks to be drawn on the y-axis.
digits_ylab: a numeric value specifying the number of digits shown for the expression levels on the y-axis.
add_expression_values: a logical value indicating whether expression values should be displayed on the plot.
n_genes_for_distance: a numeric value specifying the number of top genes to be selected based on the highest distance sum.
...: additional parameters passed to matplot.

Details

This function simply visualizes or subsets the gene expression levels of a set of genes that are stored in the input ExpressionSet.

Author

Hajk-Georg Drost and Filipa Martins Costa

Examples

data(PhyloExpressionSetExample)

# the best parameter setting to visualize this plot:
# png("test_png.png",700,400)
PlotGeneSet(ExpressionSet = PhyloExpressionSetExample, 
            gene_set      = PhyloExpressionSetExample[1:5, 2], 
            lty           = 1, 
            lwd           = 4,
            xlab          = "Ontogeny",
            ylab          = "Expression Level")
#> Error in PlotGeneSet(ExpressionSet = PhyloExpressionSetExample, gene_set = PhyloExpressionSetExample[1:5,     2], lty = 1, lwd = 4, xlab = "Ontogeny", ylab = "Expression Level"): argument "gene.set" is missing, with no default

# dev.off()

# In case you would like to work with the expression levels
# of selected genes you can specify the 'get_subset' argument:

plot_gene_set(ExpressionSet = PhyloExpressionSetExample, 
            gene_set      = PhyloExpressionSetExample[1:5, 2], 
            get_subset    = TRUE)
#> Error in plot_gene_set(ExpressionSet = PhyloExpressionSetExample, gene_set = PhyloExpressionSetExample[1:5,     2], get_subset = TRUE): could not find function "plot_gene_set"


# get a gene subset using only a phylostratihraphic map
ExamplePSMap <- PhyloExpressionSetExample[ , 1:2]

plot_gene_set(ExpressionSet = ExamplePSMap, 
            gene_set      = PhyloExpressionSetExample[1:5, 2], 
            get_subset    = TRUE,
            use_only_map  = TRUE)
#> Error in plot_gene_set(ExpressionSet = ExamplePSMap, gene_set = PhyloExpressionSetExample[1:5,     2], get_subset = TRUE, use_only_map = TRUE): could not find function "plot_gene_set"
            
# In case you want the expression values to appear for the 2 genes with a most differentiated profile
plot_gene_set(ExpressionSet = PhyloExpressionSetExample, 
            gene_set      = PhyloExpressionSetExample[1:5, 2], 
            add_expression_values =T,
            n_genes_for_distance = 2
            )
#> Error in plot_gene_set(ExpressionSet = PhyloExpressionSetExample, gene_set = PhyloExpressionSetExample[1:5,     2], add_expression_values = T, n_genes_for_distance = 2): could not find function "plot_gene_set"