cohort_heatmap: Generate heatmap plot for the given tissue and module. If the...

In vdumeaux/mixtApp: Matched Interaction across Tissues (MIxT) data analysis

Generate heatmap plot for the given tissue and module. If the heatmap already exists, it finds the appropriate png file where it is supposed to store a new one, it returns this file. This heat map function generates both a png and a pdf. All plots are stored in the path given by 'imgpath'

Description

Generate heatmap plot for the given tissue and module. If the heatmap already exists, it finds the appropriate png file where it is supposed to store a new one, it returns this file. This heat map function generates both a png and a pdf. All plots are stored in the path given by 'imgpath'

Usage

cohort_heatmap(tissue, module, cohort.name = "all",
  orderByModule = NULL, orderByTissue = NULL, cl.height = 6)

Arguments

tissue	we want to look at
module	the module we want to generate a heetmap for
cohort.name	the patient cohort we select patients from, defaults to all patients
orderByModule	which module we want to order patients by. Default is order by module.
orderByTissue	the tissue where the orderByModule module is found. Default is the same tissue.
cl.height	dimension of plotting area for clinical variable. Default = 6

Examples

cohort_heatmap("blood", "green")
cohort_heatmap("biopsy", "blue")

vdumeaux/mixtApp documentation built on Oct. 10, 2024, 3:18 a.m.