Top used analysesΒΆ

dr.survival.uni
Univariable survival analysis between a molecular variable and patient overall survival (os), profression-free survival (pfs), disease-free survival (dfs), and etc.
dr.diff
Differential analysis using rank sum test (Wilcoxon or Kruskal-Wallis, default) or student t-test in 2 or more than 2 groups.
dr.corr
Pearson or spearman (default) correlation analysis between two variables.
dr.mutcount
Mutation count barplot. Can group by any clinical features such as ER, PR, Her2 status if available.
dr.mutenrich
Driver mutation enrichment analysis. This analysis calculates whether a gene mutation is enriched in two different patient cohorts (e.g. ER+ vs. ER-). Chi-square test is performed.
dr.mutsignature
Mutation signature summary heatmap. Hierarchical clustering is performed by default.
dr.caterpillar
Caterpillar plot can be used to visualize mutation count, number of neoantigens, and any other numeric variables.
dr.lollipop
Mutation lollipop. If mutation happened in coding genes, uniprot canonical protein sequence and pfam domain annotation is annotated as x asix. If mutation happened in non-coding regions, chromosome position is used to show mutation positions.
dr.scatterbox
Boxplot with scatter dots. Can be applied to visualize number of samples, mutation counts, number of neoantigens and any numeric varibales.
dr.stackedbar
Stacked barplot. Can be used to visualize mutation signatures and any numeric variables.
dr.piechart
Piechart is used to summarize categorical varibales in a sample cohort, such as gender, stage, grade, tissue, race, etc.
dr.histogram
Histogram plot is used to summarize numeric varibales in a sample cohort, such as age, survival time, inital diagnosed time, etc.
dr.waterfall
Waterfall plot (mutation landscape) visualizes the mutation and copy number variation in a sample cohort.