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

Description Usage Arguments Details Value See Also Examples

Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap

pheatmap(mat,
    color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100),
    kmeans_k = NA,
    breaks = NA,
    border_color = "grey60",
    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 = "Matrix",
    ...)

`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`	Not supported.
`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`.
`...`	Other arguments passed to `Heatmap`.