im_boxplot_tcga: Generates a stratified boxplot for immune feature values...
In Bozorgui/imogene: : Immuno-oncology gene expression associations

Description Usage Arguments Details Value See Also Examples

Generates a stratified boxplot for immune feature values based of a two genes.

im_boxplot_tcga(
  onco_gene,
  icp_gene,
  cohort,
  Immune_phenotype,
  sample_list,
  logtrans
)

`onco_gene`	A character indicating a single onco_gene Hugo symbol.
`icp_gene`	A character indicating a single immune checkpoint Hugo symbol.
`cohort`	a single TCGA disease
`Immune_phenotype`	an immune phenotype name as listed in TCGA_Immune_phenotypes_list.
`sample_list`	An optional character vector of TCGA samples barcodes indicating a subset of samples within a cohort. All barcodes in sample_list must be 15 character long and belong to the same cohort.
`logtrans`	An optional logical indicating if y axis should be displayed in logarithmic scale. Default is FALSE.

Feature data is stratified based on expression quartiles of onco_gene and icp_gene. High/Low categories include samples with expression values in lower/upper quartiles correspondingly. Samples with expression values in middle quartiles are discarded. For details of quartile calculation see get_quantile_rank function.

Pvalues are calculated using Wilcoxon test.

a list of multiple dataframes of correlation coefficients and p.values

get_quantile_rank