plot_survival: Forest plot of survial analysis by ImSig

In imsig: Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours

Description

Patients are split into two groups based on their immune cell abundance (median aundance value) and a regular survival analyis is carried out. Raw values can be obtained from imsig_survival.

Usage

plot_survival(exp, cli, time = "time", status = "status", r = 0.6)

Arguments

exp	Dataframe of transcriptomic data (natural scale) containing genes as rows and samples as columns. Note: Gene names should be set as row names and duplicates are not allowed. Missing values are not allowed within the expression matrix. Check example- head(example_data): example_data.
cli	Clinical metadata containting the event data (dead or alive) and time to event data. Samples names should be in rownames and same as that in the expression file. Check head() of example_cli for an example clinical data.
time	Column name of time-to-event parameter.
status	Column name of event (dead or alive) parameter.
r	Use a value between 0 and 1. Default is 0.6. This is a user defined correlation cut-off to perform feature selection (feature_select). Feature selection aids to enrich the prediction of relative abundance of immune cells by filtering off poorly correlated ImSig genes. To get an idea of what cut-off to use check the results of (gene_stat) and choose a cut-off that displays high median correlation and maintains a high proportion of genes after feature selection.

Value

Forest plot

See Also

feature_select, example_data, example_cli

Examples

plot_survival (exp = example_data, r = 0.7, cli = example_cli, time = 'time', status= 'status')

Example output

Warning messages:
1: Use of `surv_data$`Log2-Hazard ratio of low expression`` is discouraged. Use `Log2-Hazard ratio of low expression` instead. 
2: Use of `surv_data$`95% CI lower limit`` is discouraged. Use `95% CI lower limit` instead. 
3: Use of `surv_data$`95% CI upper limit`` is discouraged. Use `95% CI upper limit` instead. 
4: Use of `surv_data$p` is discouraged. Use `p` instead. 

imsig documentation built on Jan. 13, 2021, 9:51 p.m.