pheatmap: Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap
In jokergoo/ComplexHeatmap: Make Complex Heatmaps

pheatmap

R Documentation

Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap

Description

Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap

Usage

pheatmap(mat,
    color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100),
    kmeans_k = NA,
    breaks = NA,
    border_color = ifelse(nrow(mat) < 100 & ncol(mat) < 100, "grey60", NA),
    cellwidth = NA,
    cellheight = NA,
    scale = "none",
    cluster_rows = TRUE,
    cluster_cols = TRUE,
    clustering_distance_rows = "euclidean",
    clustering_distance_cols = "euclidean",
    clustering_method = "complete",
    clustering_callback = NA,
    cutree_rows = NA,
    cutree_cols = NA,
    treeheight_row = ifelse(class(cluster_rows) == "hclust" || cluster_rows, 50, 0),
    treeheight_col = ifelse(class(cluster_cols) == "hclust" || cluster_cols, 50, 0),
    legend = TRUE,
    legend_breaks = NA,
    legend_labels = NA,
    annotation_row = NA,
    annotation_col = NA,
    annotation = NA,
    annotation_colors = NA,
    annotation_legend = TRUE,
    annotation_names_row = TRUE,
    annotation_names_col = TRUE,
    drop_levels = TRUE,
    show_rownames = TRUE,
    show_colnames = TRUE,
    main = NA,
    fontsize = 10,
    fontsize_row = fontsize,
    fontsize_col = fontsize,
    angle_col = c("270", "0", "45", "90", "315"),
    display_numbers = FALSE,
    number_format = "%.2f",
    number_color = "grey30",
    fontsize_number = 0.8 * fontsize,
    gaps_row = NULL,
    gaps_col = NULL,
    labels_row = NULL,
    labels_col = NULL,
    filename = NA,
    width = NA,
    height = NA,
    silent = FALSE,
    na_col = "#DDDDDD",
    name = NULL,
    
    # other graphic parameters for fonts
    fontfamily = "",
    fontfamily_row = fontfamily,
    fontfamily_col = fontfamily,
    fontface = 1,
    fontface_row = fontface,
    fontface_col = fontface,
    
    # argument specific for Heatmap()
    heatmap_legend_param = list(),
    ...,
    run_draw = FALSE)

Arguments

`mat`	The input matrix.
`color`	The same as in `pheatmap`. Here you don't necessarily need to generate a long color vector. The discrete colors sent to `colorRampPalette` are also OK here. E.g. `colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100)` can be simply replaced as `rev(brewer.pal(n = 7, name = "RdYlBu"))`.
`kmeans_k`	The same as in `pheatmap`.
`breaks`	The same as in `pheatmap`.
`border_color`	The same as in `pheatmap`.
`cellwidth`	The same as in `pheatmap`.
`cellheight`	The same as in `pheatmap`.
`scale`	The same as in `pheatmap`.
`cluster_rows`	The same as in `pheatmap`.
`cluster_cols`	The same as in `pheatmap`.
`clustering_distance_rows`	The same as in `pheatmap`.
`clustering_distance_cols`	The same as in `pheatmap`.
`clustering_method`	The same as in `pheatmap`.
`clustering_callback`	The same as in `pheatmap`.
`cutree_rows`	The same as in `pheatmap`.
`cutree_cols`	The same as in `pheatmap`.
`treeheight_row`	The same as in `pheatmap`.
`treeheight_col`	The same as in `pheatmap`.
`legend`	The same as in `pheatmap`.
`legend_breaks`	The same as in `pheatmap`.
`legend_labels`	The same as in `pheatmap`.
`annotation_row`	The same as in `pheatmap`.
`annotation_col`	The same as in `pheatmap`.
`annotation`	The same as in `pheatmap`.
`annotation_colors`	The same as in `pheatmap`.
`annotation_legend`	The same as in `pheatmap`.
`annotation_names_row`	The same as in `pheatmap`.
`annotation_names_col`	The same as in `pheatmap`.
`drop_levels`	Enforced to be `TRUE`.
`show_rownames`	The same as in `pheatmap`.
`show_colnames`	The same as in `pheatmap`.
`main`	The same as in `pheatmap`.
`fontsize`	The same as in `pheatmap`.
`fontsize_row`	The same as in `pheatmap`.
`fontsize_col`	The same as in `pheatmap`.
`angle_col`	The same as in `pheatmap`.
`display_numbers`	The same as in `pheatmap`.
`number_format`	The same as in `pheatmap`.
`number_color`	The same as in `pheatmap`.
`fontsize_number`	The same as in `pheatmap`.
`gaps_row`	The same as in `pheatmap`.
`gaps_col`	The same as in `pheatmap`.
`labels_row`	The same as in `pheatmap`.
`labels_col`	The same as in `pheatmap`.
`filename`	Not supported.
`width`	Not supported.
`height`	Not supported.
`silent`	Not supported.
`na_col`	The same as in `pheatmap`.
`name`	Name of the heatmap. This argument is passed to `Heatmap`.
`fontfamily`	Font family for row and column names.
`fontfamily_row`	Font family for row names.
`fontfamily_col`	Font family for column names.
`fontface`	Font face for row and column names.
`fontface_row`	Font face for row names.
`fontface_col`	Font face for column names.
`heatmap_legend_param`	Pass to `Heatmap`.
`...`	Other arguments passed to `Heatmap`.
`run_draw`	Whether to run `draw()` function to the heatmap object.