Function reference • teal.modules.hermes

Package

teal.modules.hermes-package: teal.modules.hermes Package

Utility Functions

h_assign_to_group_list(): Helper Function For Group List Creation

h_collapse_levels(): Helper Function for Collapsing of Factor Levels

h_extract_words(): Helper Function to Extract Words

h_gene_data(): Helper Function to Format Gene Choices

h_km_mae_to_adtte(): Data Preprocessing for ADTTE Module

h_order_genes(): Helper Function to Order Gene Choices

h_parse_genes(): Helper Function to Parse Genes

h_update_gene_selection(): Helper Function to Update Gene Selection

is_blank(): Checking for Empty String

Shiny Modules

adtteSpecInput(): Module Input for ADTTE Specification

adtteSpecServer(): Module Server for ADTTE Specification

assaySpecInput(): Module Input for Assay Specification

assaySpecServer(): Module Server for Assay Specification

experimentSpecInput(): Module Input for Experiment Specification

experimentSpecServer(): Module Server for Experiment Specification

geneSpecInput(): Module Input for Gene Signature Specification

geneSpecServer(): Module Server for Gene Signature Specification

sampleVarSpecInput(): Module Input for Sample Variable Specification

sampleVarSpecServer(): Module Server for Sample Variable Specification

multiSampleVarSpecServer(): Module Server for Specification of Multiple Sample Variables

Teal Module Functions

tm_g_barplot() ui_g_barplot() srv_g_barplot() sample_tm_g_barplot(): Teal Module for RNA-seq Barplot

tm_g_boxplot() ui_g_boxplot() srv_g_boxplot() sample_tm_g_boxplot(): Teal Module for RNA-seq Boxplot

tm_g_forest_tte() ui_g_forest_tte() srv_g_forest_tte() sample_tm_g_forest_tte(): Teal Module for Survival Forest Plot

tm_g_km() ui_g_km() srv_g_km() sample_tm_g_km(): Teal Module for Kaplan-Meier Plot

tm_g_pca() ui_g_pca() srv_g_pca() sample_tm_g_pca(): Teal Module for PCA Analysis

tm_g_quality() ui_g_quality() srv_g_quality() sample_tm_g_quality(): Teal Module for RNA-seq Quality Control

tm_g_scatterplot() ui_g_scatterplot() srv_g_scatterplot() sample_tm_g_scatterplot(): Teal Module for RNA-seq Scatterplot

tm_g_volcanoplot() ui_g_volcanoplot() srv_g_volcanoplot() sample_tm_g_volcanoplot(): Teal Module for RNA-seq Volcano Plot

Graph Functions

heatmap_plot(): Correlation Heatmap Plot

top_gene_plot(): Most Expressed Genes Plot

Assertions

assert_adtte_vars(): Check for ADTTE Variables

check_reactive() assert_reactive() test_reactive(): Check for Reactive Input

assert_summary_funs(): Check for List of Summary Functions

check_tag() assert_tag() test_tag() expect_tag(): Check for Shiny Tag

Validations

validate_gene_spec(): Validation of Gene Specification

validate_n_levels(): Validation of Number of Levels