plot_exposures {YAPSA} | R Documentation |
plot_exposures
: The exposures H
, determined by NMF or by
LCD
, are displayed as a stacked barplot by calling
The x-axis displays the PIDs (patient
identifier or sample), the y-axis the counts attributed to the different
signatures with their respective colours per PID. Is called by
plot_relative_exposures
.
plot_relative_exposures
: Plot the relative or normalized exposures of
a cohort. This function first normalizes its input and then sends the
normalized data to plot_exposures
.
plot_exposures( in_exposures_df, in_signatures_ind_df, in_subgroups_df = NULL, in_sum_ind = NULL, in_subgroups.field = "subgroup", in_title = "", in_labels = TRUE, in_show_subgroups = TRUE, legend_height = 10 ) plot_relative_exposures( in_exposures_df, in_signatures_ind_df, in_subgroups_df, in_sum_ind = NULL, in_subgroups.field = "subgroup", in_title = "", in_labels = TRUE, in_show_subgroups = TRUE )
in_exposures_df |
Numerical data frame encoding the exposures |
in_signatures_ind_df |
A data frame containing meta information about the signatures |
in_subgroups_df |
A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup |
in_sum_ind |
Index vector influencing the order in which the PIDs are going to be displayed |
in_subgroups.field |
String indicating the column name in
|
in_title |
Title for the plot to be created. |
in_labels |
Flag, if |
in_show_subgroups |
Flag, if |
legend_height |
How many signatures should be displayed in one column together at most. |
The generated barplot - a ggplot2 plot
data(lymphoma_cohort_LCD_results) plot_exposures(lymphoma_Nature2013_COSMIC_cutoff_exposures_df, chosen_signatures_indices_df, COSMIC_subgroups_df) data(lymphoma_cohort_LCD_results) plot_relative_exposures(lymphoma_Nature2013_COSMIC_cutoff_exposures_df, chosen_signatures_indices_df, COSMIC_subgroups_df)