HeatmapView | R Documentation |
Draw heatmap
HeatmapView(
mat,
breaks = c(-2, 0, 2),
colors = c("blue", "#EEEEEE", "red"),
na_col = "grey",
cluster_rows = FALSE,
row_dend_side = c("left", "right"),
cluster_cols = FALSE,
column_dend_side = c("top", "bottom"),
show_row_names = TRUE,
row_names_side = "left",
row_names_gp = gpar(fontsize = 12),
row_names_rot = 0,
show_column_names = TRUE,
column_names_side = "bottom",
column_names_gp = gpar(fontsize = 12),
column_names_rot = 90,
show_legend = TRUE,
top_ann = NULL,
top_ann_col = NULL,
show_top_legend = show_legend,
bott_ann = NULL,
bott_ann_col = NULL,
show_bott_legend = show_legend,
left_ann = NULL,
left_ann_col = NULL,
show_left_legend = show_legend,
right_ann = NULL,
right_ann_col = NULL,
show_right_legend = show_legend,
show_ann_name = FALSE,
row_split = NULL,
column_split = NULL,
show_heatmap_legend = TRUE,
legend_title = NULL,
legend_title_position = "lefttop",
legend_direction = "vertical",
legend_title_gp = gpar(fontsize = 12),
legend_labels_gp = gpar(fontsize = 12),
legend_height = 2,
legend_width = 0.3,
legend_side = "right",
...
)
mat |
Matrix like object |
breaks |
A vector indicating numeric breaks |
colors |
A vector of colors which correspond to values in breaks |
na_col |
Color for NA values. |
cluster_rows |
Same as that in ComplexHeatmap::Heatmap. |
row_dend_side |
Same as that in ComplexHeatmap::Heatmap. |
cluster_cols |
Same as that in ComplexHeatmap::Heatmap. |
column_dend_side |
Same as that in ComplexHeatmap::Heatmap. |
show_row_names |
Same as that in ComplexHeatmap::Heatmap. |
row_names_side |
Same as that in ComplexHeatmap::Heatmap. |
row_names_gp |
Same as that in ComplexHeatmap::Heatmap. |
row_names_rot |
Same as that in ComplexHeatmap::Heatmap. |
show_column_names |
Same as that in ComplexHeatmap::Heatmap. |
column_names_side |
Same as that in ComplexHeatmap::Heatmap. |
column_names_gp |
Same as that in ComplexHeatmap::Heatmap. |
column_names_rot |
Same as that in ComplexHeatmap::Heatmap. |
show_legend |
Whether show annotation legends. |
top_ann |
A data frame. Each column will be treated as a simple annotation. The data frame must have column names. Can also be a HeatmapAnnotation-class object. |
top_ann_col |
A list of colors which contain color mapping to df. |
show_top_legend |
Whether show annotation legends. |
bott_ann |
Same as top_ann. |
bott_ann_col |
A list of colors which contain color mapping to df. |
show_bott_legend |
Whether show annotation legends. |
left_ann |
Same as top_ann. |
left_ann_col |
A list of colors which contain color mapping to df. |
show_left_legend |
Whether show annotation legends. |
right_ann |
Same as top_ann. |
right_ann_col |
A list of colors which contain color mapping to df. |
show_right_legend |
Whether show annotation legends. |
show_ann_name |
Whether show annotation names. |
row_split |
A vector or a data frame by which the rows are split. But if cluster_rows is a clustering object, split can be a single number indicating to split the dendrogram by cutree. |
column_split |
Same as row_split. |
show_heatmap_legend |
Whether show legends. |
legend_title |
Character specifyin the legend title. |
legend_title_position |
Position of title relative to the legend. topleft, topcenter, leftcenter-rot and lefttop-rot are only for vertical legend and leftcenter, lefttop are only for horizontal legend. |
legend_direction |
Vertical or horizontal? |
legend_title_gp |
Graphic parameters of the title. |
legend_labels_gp |
Graphic parameters for labels. |
legend_height |
Height of the whole legend body. It is only used for vertical continous legend. |
legend_width |
Width of the whole legend body. It is only used for horizontal continous legend. |
legend_side |
Side to put heatmap legend |
... |
Other parameters in draw. |
No return.
Wubing Zhang
dat = matrix(rnorm(100), 10)
rownames(dat) = letters[1:10]
colnames(dat) = letters[11:20]
rowann = data.frame(Group = rep(letters[1:2], each=5), index = 1:10)
colann = data.frame(Group = rep(letters[1:2], each=5), index = 11:20)
HeatmapView(dat, left_ann = rowann, top_ann = colann)
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