Man pages for edawson/tidysig
Plot mutational signatures using ggplot objects
| add_val_buffer | Add some amount of buffer to a value. Used to calculate the... |
| calculate_smart_ylimits | Returns a set of ylimits trimmed to fit the input dataframe. |
| combine_context_change_cols | A helper function to 1. Properly rename columns in... |
| convert_pcawg_to_sigprofiler_SBS96 | Convert a pcawg-formatted dataframe to modern sigprofiler... |
| determine_context | A helper function to determine the context type of a... |
| drop_enforced_signatures | Remove enforced signatures from a dataframe |
| export_to_signatureanalyzer_word_SBS96 | Transform a tibble in TidySig format to SigantureAnalyzer's... |
| export_to_sigprofiler_SBS96 | Convert a Tidy-formatted tibble to the SigProfiler matrix... |
| generate_plot | A helper function for plotting ID83 / SBS96 plots. |
| get_maximum_amount | Retrieve the maximum value of a signature or activity... |
| get_minimum_amount | Retrieve the minimum value of a signature or activity... |
| id_83_colors | A color palette for ID83 changes. Matches that of... |
| load_pandas_hdf5_data | Loads a Pandas data frame, restricting to a top level path... |
| normalize_counts | Transform per-signature feature counts to proportions |
| normalize_sample_counts | Convert per-sample counts to proportions |
| per_sample_counts_summary | Generate a sample-level summary of Signature counts |
| per_sample_proportions_summary | Generate a sample-level summary of Signature proportions |
| per_sample_summary | Generate a sample-level summary of Signature counts and... |
| plot_activities | Plot the activities of signature(s) |
| plot_context | A helper function to plot mutational contexts, which are... |
| plot_ID83_signature | Plot an ID83 signature ro series of signatures |
| plot_SBS96_signature | Plot an SBS96 signature or series of signatures |
| plot_signature | Plot an ID83 signature ro series of signatures |
| read_pcawg_SBS96_csv | Read in a PCAWG-format CSV file |
| save_signature_plot | Save a plot for a single mutational signature |
| sbs_96_changes | A list of the six possible (normalized) SBS96 mutational... |
| sbs_96_changes_colors | A color palette for SBS96 changes. Matches that of... |
| sbs_96_contexts | A list of the SBS96 mutational contexts |
| signature_activity_figure | Plot the activities of signature(s) as both counts and... |
| tidysig | 'tidysig' package |
| tidy_sigprof_activities | Transform sigprofiler activities into TidySig format |
| tidy_sigprof_ID83_df | A wrapper around transform_sigprofiler_df for legacy... |
| tidy_sigprof_id83_probabilities | A fuction for formatting the signature probability files of... |
| tidy_sigprof_SBS96_df | A wrapper around transform_sigprofiler_df for legacy... |
| tidy_sigprof_sbs96_probabilities | A fuction for formatting the signature probability files of... |
| transform_sigprofiler_df | Transform a Sigprofiler dataframe (of counts, percentages,... |
| transpose_sigprofiler_df | Transpose a SigProfiler dataframe |
