pheatmap2: Pretty and parallel heatmap
In jokergoo/pheatmap2: Pretty Plus Parallel Heatmap

Description Usage Arguments Details

View source: R/pheatmap2.R

Pretty and parallel heatmap

pheatmap2(mat,
    col_fun = colorRamp2(breaks = seq(min(mat), max(mat), length = 7),
    colors = rev(brewer.pal(n = 7, name = "RdYlBu"))),
    mat_list = NULL, col_fun_list = NULL, gap = rep(1, length(mat_list)),
    cluster_rows = TRUE, cluster_cols = TRUE,
    clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean",
    clustering_method = "complete",
    legend_title = "Main matrix", legend_title_list = NULL,
    annotation = NULL, annotation_colors = NULL,
    show_rownames = TRUE, show_colnames = TRUE, main = NULL,
    annotation_list = NULL, annotation_colors_list = NULL,
    show_legend = TRUE, show_annotation_legend = TRUE, sub_main = NULL,
    newpage = TRUE, ...)

`mat`	main matrix
`col_fun`	mapping function to transform values to colors
`mat_list`	A list of additional matrix. The list should have name index
`col_fun_list`	A list of color mapping functions. The list should have name index and the name index should correspond to `mat_list`
`gap`	gaps between heatmap. It is measured by numbers of empty columns. Can be a scalar or a vector
`cluster_rows`	Logical, whether to cluster rows
`cluster_cols`	Logical, whether to cluster columns
`clustering_distance_rows`	method to cluster rows, possible values are in `dist` plus "correlation", "spearman", "mutualInfo", "tao"
`clustering_distance_cols`	same as `clustering_distance_cols`
`clustering_method`	method to do clustering. Possible values are in `hclust`
`legend_title`	the title for the legend which corresponds to the main matrix
`legend_title_list`	titles for the additional matrix.
`annotation`	A data frame, for the format of this variable, see original `pheatmap` function
`annotation_colors`	a list, for the format of this variable, see original `pheatmap` function
`show_rownames`	logical, whether to plot row names
`show_colnames`	logical, whether to plot column names
`main`	title for the plot
`annotation_list`	a list of `annotation` for additional matrix
`annotation_colors_list`	a list of `annotation_colors` for additional matrix
`show_legend`	logical, whether show legend
`show_annotation_legend`	logical whether show annotation legend
`sub_main`	sub title for each heatmap
`newpage`	whether create a new grid newpage
`...`	other arguments passed to `gpar`