visualizations

Functions to plot data from Samples object or DMPs/DMRs dataframes

Functions

analyze_replicates(samples, sample_id_column)	Analyze the beta values standard deviation of the technical replicates to check for batch effect or quality issues.
betas_2D(samples[, label_column, ...])	Plot samples in 2D space according to their beta distances.
betas_dendrogram(samples[, title, ...])	Plot dendrogram of samples according to their beta values distances.
betas_density(samples[, title, ...])	Plot beta values density for each sample
betas_heatmap(samples[, apply_mask, ...])	Plot a heatmap of the probes with the most variable beta values, showing hierarchical clustering of the probes with dendrograms on the sides.
cns_manhattan_plot(data_to_plot[, ...])	Display a Manhattan plot of the given CNS data, designed to work with the dataframes returned by copy_number_segmentation()
dmp_heatmap(dm[, contrast, nb_probes, ...])	Plot a heatmap of the probes that are the most differentially methylated, showing hierarchical clustering of the probes with dendrograms on the sides.
dmr_manhattan_plot(dm, contrast[, ...])	Display a Manhattan plot of the given DM data
metadata_correlation(input_data[, columns, ...])	Plot the correlation between the metadata columns of the samplesheet.
metadata_pairplot(input_data[, columns, ...])	Build a pair plot from the samples' sample sheet.
methylation_distribution(samples, group_column)	Plot the distribution of hyper- and hypo- methylated probes in the samples.
nb_probes_per_chr_and_type_hist(samples[, ...])	Plot the number of probes covered by the sample per chromosome and design type
pc_association_heatmap(samples[, params, ...])	Heatmap of the p-values for the association of principal components and the parameters in the sample sheet.
pc_correlation_heatmap(samples[, params, ...])	Heatmap of the correlation between principal components and the metadata of the sample sheet.
show_chromosome_legend()	Display a legend for chromosome regions colors used in the 'visualize_gene' function, corresponding to Giemsa staining.
visualize_chromosome_region(samples, ...[, ...])	Show the beta values of a gene for all probes and samples in its transcription zone.
visualize_gene(samples, gene_name[, ...])	Show the beta values of a gene for all probes and samples in its transcription zone.