plotPAM50: Visualize PAM50 Prediction

In ccchang0111/PAM50: Breast Cancer's PAM50 prediction based on patient's RNA-seq data

Description

This is to generate a heatmap to check the result of PAM50 prediction.

Usage

plotPAM50(es, PAM50.pred, add_labels = NULL, cluster_rows = F,
  cluster_cols = F, scale = "row", ...)

Arguments

es	dataframe, rows are genes columns are samples. Row names has to be EntrezID.
PAM50.pred	array of each sample's PAM50 label (you can get the label using PAM50 function)
add_labels	Additional argument for adding extra labels (dataframe) to show in the heatmap. Labels have to be the same sample order as PAM50.pred
cluster_rows	bool (defaul = False), indicate whether to reorder the genes. Default uses Parker et al. paper's gene order.
cluster_cols	bool (defaul = False), indicate whether to reorder the samples.
scale	string (default = "row"). Options are "none", "row", or "column". This is to rescale data (calculate zscore) based on row, column or no rescaling.
...	other parameters passed onto pheatmap, for instance, main = "Treatment Arms".

ccchang0111/PAM50 documentation built on May 31, 2019, 5:40 a.m.