Visulisations for methylation and expression.

Function plot_volcanoes generate a dashboard with volcano plots for expression and methylation. Also it adds a tables with basic statistics.

plot_volcanoes(data.m, data.e, condition.m, condition.e, gene = NA,
  test.m = list(), test.e = list(), values = FALSE, font.size = 6)

Arguments

data.m	Data frame containing information for methylation.
data.e	Data frame containing information for expression.
condition.m	Condition for methylation data (data.m).
condition.e	Condition for expression methylation (data.e).
gene	Gene name.
test.m	List of tests results for methylation.
test.e	List of tests results for expression
values	Logical. If TRUE p-values and log fold for chosen gene will be added to a plot. By default we use FALSE.
font.size	Font size in stats table.

Value

An object of class ggplot containing volcano plots of p-values versus log2.fold for gene for chosen number of tests. Also there are added simple statistisc about chosen gene.

See also

plot_volcano

plot_volcano

Examples

# NOT RUN {
library(MLExpRessoData)
cond_exp <- ifelse(BRCA_exp$SUBTYPE == "LumA","LumA","other")
cond_met <- ifelse(BRCA_met$SUBTYPE == "LumA","LumA","other")

BRCA_met_gen <- aggregate_probes(BRCA_met[,-1])

test1  <- calculate_test(BRCA_exp[,-1], condition_exp, test="lrt")
test2  <- calculate_test(BRCA_met_gen, condition_met, test="ttest")

plot_volcanoes(BRCA_met[,-1],BRCA_exp[,-1],cond_met, cond_exp, "ICAM2", test1, test2, values=TRUE)
# }