genericheatmap: heatmap plot for pathway

In ShouyeLiu/metaboliteUtility:

Description

heatmap plot for pathway

Usage

genericheatmap(mat, top_annotation, column_title = "", name = "",
  cluster_rows = TRUE, cluster_columns = FALSE, show_row_names = TRUE,
  show_column_names = TRUE, rect_gp = grid::gpar(col = "grey"),
  row_names_gp = grid::gpar(fontsize = 9),
  column_names_gp = grid::gpar(fontsize = 9),
  col = circlize::colorRamp2(c(-3, -1, 0, 1, 3), c("dark blue", "white",
  "red")), ...)

Arguments

mat	a matrix, please see examples

Details

Please see Heatmap

Examples

library(ComplexHeatmap)
data(heatmap_data)
metaname <- names(heatmap_data)[4:length(heatmap_data)]
subTime <- singleTime <- c("week4","week8")
tmp_dataset<- data <- metabolite_data_subset
baseline_data <-data[which(data$time %in% c("baseline")),];
dataLen <- length(baseline_data);
propData = data.frame(BL = rep(0,dataLen-3));
for (singleTime in subTime)
{
    inditmp_dataset <- tmp_dataset[which(tmp_dataset$time %in% singleTime),];
    for ( i in 4:dataLen)
    {
        inditmp_dataset[,i] <-  inditmp_dataset[,i] - baseline_data[,i];
    }
    is.na(inditmp_dataset[4:dataLen]) <- sapply(inditmp_dataset[4:dataLen],is.infinite);
    tmp_dataset2 <- as.data.frame(colMeans(inditmp_dataset[4:dataLen], na.rm = T));
    names(tmp_dataset2) <- singleTime;
    propData <- cbind(propData,tmp_dataset2 );
}
tmpMat <- as.matrix(propData[c('BL',subTime)]);
 # handle pathway info
pathwayData <- data.frame(Var= metaname,
                          Pathway = (paste0("p",sample.int(3, length(metaname), replace = TRUE))))
pathwayNum <- length(unique(pathwayData$Pathway));
groupPathwayColor <- structure(circlize::rand_color(pathwayNum),names=levels(factor(pathwayData$Pathway)));
groups <- split_df_to_list_group(pathwayData, 'Pathway');
heatmapRowAnnotation = ComplexHeatmap::rowAnnotation(df=data.frame(pathway=pathwayData$Pathway),
                                                     col = list(pathway = groupPathwayColor ));
top_annotation = ComplexHeatmap::HeatmapAnnotation(group = pathwayData$Pathway,col = list(group = groupPathwayColor),show_legend = FALSE)
# drawing heatmap plot
tmpHeatmap <- NULL
tmpHeatmap <- genericheatmap(tmpMat,
                            top_annotation,
                            column_title="Heatmap pathway analysis");
tmpHeatmap <- tmpHeatmap + heatmapRowAnnotation;
heatmapDraw <- ComplexHeatmap::draw(tmpHeatmap,
                                   show_heatmap_legend=TRUE,
                                   heatmap_legend_side = "left");

heatmapDraw

ShouyeLiu/metaboliteUtility documentation built on May 6, 2019, 9:07 a.m.