seurat_heat: Heatmap for Seurat object
In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description Usage Arguments Author(s)

Equivalent to Seurat::DoHeatmap with the addition of sidebar along the rows (features) to group them using ComplexHeatmap. However, currently, only one sidebar can be plotted for rows. There is no limit for the number of side bars for columns.

seurat_heat(
  x,
  group.by = NULL,
  color_row = NULL,
  assay = "RNA",
  slot_data = "data",
  highlight = NULL,
  highlight_names = NULL,
  show_column_names = F,
  show_row_names = T,
  show_column_anna = T,
  column_rotation = 0,
  annotation_name_side = "left",
  column_names_side = "bottom",
  column_title_side = "top",
  row_names_side = "left",
  row_title_side = "left",
  show_column_bars = T,
  row_title_fontface = "bold",
  column_title_fontface = "bold",
  cluster_columns = F,
  cluster_rows = F,
  column_split = 1,
  row_reorder_levels = NULL,
  column_reorder_levels = list(),
  reorder_column = T,
  row_scale = F,
  column_scale = F,
  center_scale = F,
  color_scale = NULL,
  default_color = F,
  quantile_val = 0.05,
  provided_color = NULL,
  AP = NULL,
  title_pos = "topleft",
  heat_name = "norm count",
  break_points = NULL,
  row_legend_labels = "DE genes",
  column_legend_labels = NULL,
  column_legend_order = NULL,
  left_HA = T,
  top_HA = T,
  row_titles = character(0),
  group_order = NULL,
  main_width = NULL,
  main_height = NULL,
  grid_height = 8,
  heat_grid_height = NULL,
  automatic = T,
  ...
)

`x`	Seurat object
`group.by`	by which feature are the cells grouped
`color_row`	a vector of gene names with the name of the vector elements being the lineages
`assay`	the Seurat assay in `x`
`highlight`	which row names to highlght
`highlight_names`	display names for the highlighted and non-highlighted groups
`show_column_names`	whether to display column names (Don't confuse it with column title, which is group name)
`show_row_names`	whether to show row names
`show_column_anna`	whether to show the category for the group names for the columns around the column color bar. There is not a similar option for rows because this function only supports one row sidebar
`column_rotation`	rotate column name labels, 90 is vertical, 0 is horizontal, there are no other choices
`annotation_name_side`	side of the annotation name for column side bar
`show_column_bars`	whether to show horizontal bars for the columns. It can be a vector of the same length as `group.by` to specify the group(s) to show the horizontal bars.
`cluster_columns`	whether to perform hierarchical clustering on columns
`cluster_rows`	whether to perform hierarchical clustering on rows
`column_split`	whether to split the columns belonging to the same group in `group.by` by a thin dividing line. '1' indicate splitting. 'NA' indicates no spliting
`row_reorder_levels`	a vector indicating the order of labels for row group names that would appear from top to bottom of the heatmap. The default is `cell_order` from the list supplied to the `AP` argument
`column_reorder_levels`	a list of vectors. Each item in the list indicates the order of each column color bar labels. Again the default is in the `AP` argument
`row_scale`	whether to perform row scaling.
`column_scale`	whether to perform column scaling.
`center_scale`	whether to put white colors half way between the min and max of the matrix. Otherwise, white color is placed at value 0.
`color_scale`	the scale of color gradient for heatmap. By default, the `heatmap_color` field of the list supplied to `AP` should define the color for min, middle and max of the dataset. Otherwise, please input a function created by `circlize::colorRamp2`
`default_color`	whether to use the default color settings of ComplexHeatmap for main matrix
`quantile_val`	if supplied, then the color gradient would not extend over the entire range of the matrix. The default 0.05 means that color gradient would extend from 5% to 95% percentile. This is to avoid outliers skewing the dynamic range of colors.
`provided_color`	a named vector where the vector contains the colors and the names indicate the group labels that would be colored by the corresponding color in the sidebar.
`AP`	a list of aesthetic parameters. The important fields include `cell_order` for ordering group labels, `gfont_fam`, `fontsize` and `heatmap_color`
`title_pos`	adjustment of legend title
`heat_name`	name of the main heatmap to appear in the legend
`break_points`	where to show values in the heatmap gradient legend
`row_legend_labels`	name of the row sidebar to appear in the legend
`column_legend_labels`	name of the column sidebar in the legend. You may supply as many items as the number of column sidebars
`left_HA`	whether to show row sidebars
`top_HA`	whether to show column sidebars
`row_titles`	whether to show row titles. choose NULL if not
`group_order`	the ordering of each column
`main_width`	width of the heatmap in cm
`main_height`	height of the heatmap in cm
`grid_height`	legend grid height, increase this value if the spacing between legend labels become too narrow
`heat_grid_height`	grid height for the color gradient legend. If NULL, it is the same as `grid_height`
`automatic`	whether the default legend generation process in ComplexHeatmap is to be used. If not, all legends will be aligned vertically and only be arranged in separate columns if the total length exceeds the heatmap length.
`slow_data`	the slot in `assay`
`reorder_columns`	whether to order the columns according to `column_reorder_levels`