Man pages for kazeera/hourglass
This Package Provides Visualizations of Annotated Numeric Data
| add_to_rowAnn | Make a custom row annotation column |
| as_numeric_factor | Converts factor to number |
| avg_dataframe | Average a dataframe with continuous and discrete variables... |
| avg_dataset | Averages a dataset object. |
| bin_vars | Replaces values in a vector that equal to certain values to a... |
| clean_colors | Cleans and returns color palette. |
| cluster_corrmat | Re-orders a correlation matrix by hierarchical clustering |
| cluster_df | Re-orders a matrix by hierarchical clustering |
| create_folder | Takes in a string and creates a new folder with that name. |
| create_plots | Create plots in a folder in streamlined approach |
| create_plots_helper | Create plots helper |
| df_to_numeric | Coerce a data.frame to a numeric.data.frame |
| evaluate_filter | Subsets a dataframe based on filters |
| get_ann_colors | Get color names from unique groups in data frame |
| get_col_gradient | Get color gradient |
| get_colors | Get color palette from input Excel file. |
| get_col_palette | Get color palette in the form of colorRampPalette functions. |
| get_comparison_name | Customize name of comparison / output folder depending on... |
| get_comparisons | Get comparisons to run from input Excel file. |
| get_datasets | Prepare dataset objects in run_hourglass function. |
| get_duplicated_cases | Subset data frame to rows that are duplicated at least once |
| get_element_colors | Get colors for a named vector based on a color palette. |
| get_feat_sets | Read in and format feat_sets. |
| get_file | Search file names |
| get_levels | Get map of levels in numeric vector |
| get_nth_part | Extracts the first (or nth) entry from each split. |
| get_outliers | Identify outliers outside of 1st and 3rd quartile by making... |
| get_paired_ds | Finds means of pairs of duplicated ids in different groups |
| get_rowAnn_color_pal | Get color palette for dataset row annotations |
| has_at.least_n.vals | Checks whether a vector has at least a certain number of non... |
| has_less.than.eq.to_NA.thres | Checks which rows or columns have number of NAs less than or... |
| impute_ds | Impute numeric matrix in dataset object |
| impute_w_mean | Imputes NA/missing values in a vector with random values... |
| impute_w_mean_df | Imputes NA/missing values in a data frame with random values... |
| load_packages | Install/load packages from library into environment |
| make_dataset_ob | Initialize a dataset object |
| make_FC.pval_df | Find p-values and fold-change (FC) for each group |
| make_FC.pval_df_helper | Find p-values and fold-change (FC) for each group |
| make_FC.pval_plot | Plot FC-p value heatmap |
| make.unique.2 | R make.unique starting in 1 |
| means_of_groups | Calculates means of a vector with discrete levels |
| medians_of_groups | Calculates medians of a vector with discrete levels |
| perform_t.test | Computes t-test between 2 groups |
| perform_wilcox | Computes Wilcoxon test between 2 groups |
| plot_corrplot | Creates correlation plot using corrplot package |
| plot_corrplotgg | Creates correlation plot using ggplot2 package |
| plot_discrete_barplot | Plot discrete bar graph. |
| plot_heatmap | Plots a heatmap |
| plot_het_barplot | Plot variation bargraph |
| plot_indiv_boxplot | Creates single box plot. |
| plot_indiv_corrscatt | Plot all correlation scatter plots for pairwise variables |
| plot_indiv_paired | Create paired plot |
| plot_overview_boxplot | Creates overview box plots. |
| plot_overview_corr_scatt | Plot overview correlation scatter plot |
| plot_profile_barplot | Plot profile bar graph |
| plot_surv_curve | Plot individual survival curve (Kaplan Meier) |
| print_unique_elements_count | Prints the number of unique elements in each column |
| pval_to_stars | Convert p-values to stars |
| read_file | Read tabular data |
| reform_ann_df | Subset data frame by columns |
| remove_outliers | Remove outliers outside of 1st and 3rd quartile by making the... |
| remove_outliers2 | Removes outliers using boxplot statistics |
| remove_outliers_df | Remove outliers outside of 1st and 3rd quartile by making the... |
| rename_column | Rename a column in a data frame. |
| run_comparison | Run analysis in streamlined approach |
| run_comparison_helper | Runs main analysis for all parameter combos specified in... |
| run_corrplot_analysis | Run correlation plot analysis |
| run_discrete_barplot_analysis | Makes discrete box plots for each parameter in column... |
| run_from_excel | Run Hourglass from single Excel file input. |
| run_het_analysis | Runs heterogeneity analysis for custom comparison, look at... |
| run_hourglass | Run Hourglass. |
| run_paired_analysis | Makes plots to look at subgroup differences within the same... |
| run_profile_barplot | Generates both fill and stacked bar plots and saves to file |
| run_surv_analysis | Iteratively plot survival curves (Kaplan Meier) |
| save_table | Print comparison data (MainComparison) + sample/patient ID as... |
| sort_dataframe | Sort a dataframe by the contents of its row (sort columnwise)... |
| sort_dataset | Sort dataset list object to specified rows and/or columns... |
| split_one.by.one | Split string and iteratively return parts pasted to first... |
| subset_by_filters | Subsets a dataframe rows based on filters |
| subset_dataframe | Subset data frame to the rows and/or columns specified |
| subset_dataset | Subset dataset list object to the rows and/or columns... |
| subset_feat_sets_ds | Subset dataset for custom analysis |
| test_Hourglass | Test Hourglass R package from py interface. |
| trim_each_part | Abbreviate elements |
| turn_off_null_devices | Closes all open file connections |
