PredictionsHeatmap: Heatmap of MM2S Subtype Predictions for Given Samples

In bhklab/MM2S: Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines

Description

This function generates a graphical heatmap of MM2S subtype predictions for samples of interest. Users are provided the option to save this heatmap as a PDF file.

Usage

PredictionsHeatmap(InputMatrix,pdf_output,pdfheight,pdfwidth)

Arguments

InputMatrix	Matrix containing the samples in rows and columns containing MM2S percentage predictions for each subtype (Gr4,Gr3,SHH,WNT, and Normal)
pdf_output	Option to save the heatmap as a PDF file
pdfheight	User-defined specification for PDF height size
pdfwidth	User-defined specification for PDF width size

Value

Generated Heatmap of MM2S subtype predictions. Samples are in rows, and prediction percentages are in columns.

Author(s)

Deena M.A. Gendoo

References

Gendoo, D. M., Smirnov, P., Lupien, M. & Haibe-Kains, B. Personalized diagnosis of medulloblastoma subtypes across patients and model systems. Genomics, doi:10.1016/j.ygeno.2015.05.002 (2015)

Manuscript URL: http://www.sciencedirect.com/science/article/pii/S0888754315000774

Examples

# Generate heatmap from already-computed predictions for the GTML Mouse Model
## load computed MM2S predictions for GTML mouse model
data(GTML_Mouse_Preds)
## Generate Heatmap
PredictionsHeatmap(InputMatrix=GTML_Mouse_Preds, pdf_output=TRUE,pdfheight=20,pdfwidth=5)

# Generate heatmap after running raw expression data through MM2S
# load Mouse gene expression data for the potential WNT mouse model
data(WNT_Mouse_Expr)
SubtypePreds<-MM2S.mouse(InputMatrix=WNT_Mouse_Expr[2:3],parallelize=1, seed = 12345)
# Generate Heatmap
PredictionsHeatmap(InputMatrix=SubtypePreds$Predictions, 
pdf_output=TRUE,pdfheight=5,pdfwidth=5)

bhklab/MM2S documentation built on Dec. 25, 2021, 10:48 a.m.