Goheatmap：带有GO条款的热图

# **Goheatmap** Heatmap with GO Terms ### Installation The **development** version can be installed from GitHub using: ``` r devtools::install_github("ilwookkim/GOheatmap") ``` ### Usage ``` r library(GOheatmap) ``` **Load example data** LAML-TCGA RNAseq data ``` r mat.file <- system.file("extdata", "mat.Rdata", package="GOheatmap") load(mat.file) ``` **Pre-treatment** Remove NA, if necessary. ``` r mat <- data.frame(na.omit(mat)) knitr::kable(head(mat[, 1:4], 3), "simple") # column: samples, row: genes (HGNC symbol) TCGA.AB.2803.03 TCGA.AB.2805.03 TCGA.AB.2806.03 TCGA.AB.2807.03 ----- ---------------- ---------------- ---------------- ---------------- AGO1 1758.2305 4728.2463 2947.8039 2831.1817 AGO2 367.2840 771.7537 1113.3036 1076.4647 AGO3 727.3663 1237.6171 896.2444 965.2433 ``` **Run goheatmap** Parameters k (number of clustering), n_go (number of terms to display), sources [details here](https://biit.cs.ut.ee/gprofiler/page/apis), cor (TRUE for spearman's correlation coefficient, FALSE for z-score normalization), title (Title of heatmap) ``` r goheatmap(mat, k = 3, n_go = 3, sources = "GO:BP", cor = TRUE, title = "GOheatmap") goheatmap(mat, k = 3, n_go = 3, sources = "KEGG", cor = TRUE, title = "GOheatmap") goheatmap(mat, k = 3, n_go = 3, sources = "WP", cor = TRUE, title = "GOheatmap") ``` <img src="inst/extdata/example_go.bp.png"/> <img src="inst/extdata/example_kegg.png"/> <img src="inst/extdata/example_wp.png"/>