im_boxplot: Generate a stratified boxplot for immune feature values
In Bozorgui/imogene: : Immuno-oncology gene expression associations

Description Usage Arguments Details Value Examples

Generate a stratified boxplot for immune feature values

1	im_boxplot(onco_gene, icp_gene, data_expression, data_feature)

`onco_gene`	A charachter indicating a single onco_gene ID.
`icp_gene`	A charachter indicating a single immune checkpoint ID.
`data_expression`	A numeric matrix or data frame containing gene/protein expressions
`data_feature`	A numeric matrix or data frame containing a single immune feature.

Feature data is stratified base 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.

data_expression is formatted with genes/proteins as rows and samples/patients as columns. For data_expression sample formats see sample_mRNA_data.

data_feature is formatted with samples/patients as rows and immune feature as single column. For data_feature sample format see sample_Leukocyte_fraction_data.

a stratified boxplot

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im_boxplot(onco_gene = "TGFB1",icp_gene="TNFSF4",
                  data_expression =  sample_mRNA_data,
                  data_feature = sample_Leukocyte_fraction_data)