plot_abundance: Plot relative abundance of immune cells

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

Description

Barplots of relative abundance of immune cells across samples.The order of the samples are the same as that of imsig.

Usage

plot_abundance(exp, 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.

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

ggplot

See Also

feature_select, example_data

Examples

plot_abundance (exp = example_data, r = 0.7)

Example output

Warning messages:
1: Use of `cell$samples` is discouraged. Use `samples` instead. 
2: Use of `cell$samples` is discouraged. Use `samples` instead. 
3: Use of `cell$samples` is discouraged. Use `samples` instead. 
4: Use of `cell$samples` is discouraged. Use `samples` instead. 
5: Use of `cell$samples` is discouraged. Use `samples` instead. 
6: Use of `cell$samples` is discouraged. Use `samples` instead. 
7: Use of `cell$samples` is discouraged. Use `samples` instead. 
8: Use of `cell$samples` is discouraged. Use `samples` instead. 
9: Use of `cell$samples` is discouraged. Use `samples` instead. 
10: Use of `cell$samples` is discouraged. Use `samples` instead. 

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