visualize_data {BUScorrect} | R Documentation |
Use "heatmap.2" in R package "gplots" to visualize the gene expression data across multiple batches.
visualize_data(Data, title_name="Heatmap", gene_ind_set, color_key_range=seq(-0.5,8.5,1))
Data |
The gene expression data, an R list with length equal to the batch number. Each of its element is a gene expression matrix, where rows are genes and columns represent samples. |
title_name |
The title name of the heatmap. |
gene_ind_set |
The indices of the set of genes the user wants to display in the heatmap. |
color_key_range |
The color range in the color key. |
The values displayed in the heatmap are the raw values in the argument Data
without scaling.
visualize the gene expression data matrix, where one row is a gene and one column represents a sample.
Xiangyu Luo
Xiangyu Luo, Yingying Wei. Batch Effects Correction with Unknown Subtypes. Journal of the American Statistical Association. Accepted.
rm(list = ls(all = TRUE)) set.seed(123) #a toy example, there are 6 samples and 20 genes in each batch example_Data <- list() #batch 1 example_Data[[1]] <- rbind(matrix(c(1,1,5,5,10,10, 3,3,7,7,12,12), ncol=6, byrow=TRUE), matrix(c(1,2),nrow=18, ncol=6)) #batch 2 batch2_effect <- c(2,2,2,1,1) example_Data[[2]] <- rbind(matrix(c(1,1,5,5,10,10, 3,3,7,7,12,12), ncol=6, byrow=TRUE), matrix(c(1,2),nrow=18, ncol=6)) + batch2_effect #batch 3 batch3_effect <- c(3,2,1,1,2) example_Data[[3]] <- rbind(matrix(c(1,1,5,5,10,10, 3,3,7,7,12,12), ncol=6, byrow=TRUE), matrix(c(1,2),nrow=18, ncol=6)) + batch3_effect visualize_data(example_Data, title_name="Heatmap", gene_ind_set = 1:20, color_key_range=seq(0,10,2))