plot_lr_heatmap: Function to plot a UMAP of context loadings

In saezlab/ligrec_decoupler: LIANA: a LIgand-receptor ANalysis frAmework

Function to plot a UMAP of context loadings

Description

Function to plot a UMAP of context loadings

Usage

plot_lr_heatmap(sce, lr_sep = "^", n = 5, ...)

Arguments

sce	SingleCellExperiment with factors output from tensor-cell2cell
n	Number of rows to return for top_n(), fraction of rows to return for top_frac(). If n is positive, selects the top rows. If negative, selects the bottom rows. If x is grouped, this is the number (or fraction) of rows per group. Will include more rows if there are ties.
...	Arguments passed on to ComplexHeatmap::Heatmap matrix A matrix. Either numeric or character. If it is a simple vector, it will be converted to a one-column matrix. col A vector of colors if the color mapping is discrete or a color mapping function if the matrix is continuous numbers (should be generated by colorRamp2). If the matrix is continuous, the value can also be a vector of colors so that colors can be interpolated. Pass to ColorMapping. For more details and examples, please refer to https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#colors . name Name of the heatmap. By default the heatmap name is used as the title of the heatmap legend. na_col Color for NA values. rect_gp Graphic parameters for drawing rectangles (for heatmap body). The value should be specified by gpar and fill parameter is ignored. color_space The color space in which colors are interpolated. Only used if matrix is numeric and col is a vector of colors. Pass to colorRamp2. border Whether draw border. The value can be logical or a string of color. border_gp Graphic parameters for the borders. If you want to set different parameters for different heatmap slices, please consider to use decorate_heatmap_body. cell_fun Self-defined function to add graphics on each cell. Seven parameters will be passed into this function: j, i, x, y, width, height, fill which are column index, row index in matrix, coordinate of the cell, the width and height of the cell and the filled color. x, y, width and height are all unit objects. layer_fun Similar as cell_fun, but is vectorized. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#customize-the-heatmap-body . jitter Random shifts added to the matrix. The value can be logical or a single numeric value. It it is TRUE, random values from uniform distribution between 0 and 1e-10 are generated. If it is a numeric value, the range for the uniform distribution is (0, jitter). It is mainly to solve the problem of "Error: node stack overflow" when there are too many identical rows/columns for plotting the dendrograms. ADD: From version 2.5.6, the error of node stack overflow has been fixed, now this argument is ignored. row_title Title on the row. row_title_side Will the title be put on the left or right of the heatmap? row_title_gp Graphic parameters for row title. row_title_rot Rotation of row title. Only 0, 90, 270 are allowed to set. column_title Title on the column. column_title_side Will the title be put on the top or bottom of the heatmap? column_title_gp Graphic parameters for column title. column_title_rot Rotation of column titles. Only 0, 90, 270 are allowed to set. cluster_rows If the value is a logical, it controls whether to make cluster on rows. The value can also be a hclust or a dendrogram which already contains clustering. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#clustering . cluster_row_slices If rows are split into slices, whether perform clustering on the slice means? clustering_distance_rows It can be a pre-defined character which is in ("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman", "kendall"). It can also be a function. If the function has one argument, the input argument should be a matrix and the returned value should be a dist object. If the function has two arguments, the input arguments are two vectors and the function calculates distance between these two vectors. clustering_method_rows Method to perform hierarchical clustering, pass to hclust. row_dend_side Should the row dendrogram be put on the left or right of the heatmap? row_dend_width Width of the row dendrogram, should be a unit object. show_row_dend Whether show row dendrogram? row_dend_gp Graphic parameters for the dendrogram segments. If users already provide a dendrogram object with edges rendered, this argument will be ignored. row_dend_reorder Apply reordering on row dendrograms. The value can be a logical value or a vector which contains weight which is used to reorder rows. The reordering is applied by reorder.dendrogram. cluster_columns Whether make cluster on columns? Same settings as cluster_rows. cluster_column_slices If columns are split into slices, whether perform clustering on the slice means? clustering_distance_columns Same setting as clustering_distance_rows. clustering_method_columns Method to perform hierarchical clustering, pass to hclust. column_dend_side Should the column dendrogram be put on the top or bottom of the heatmap? column_dend_height height of the column cluster, should be a unit object. show_column_dend Whether show column dendrogram? column_dend_gp Graphic parameters for dendrogram segments. Same settings as row_dend_gp. column_dend_reorder Apply reordering on column dendrograms. Same settings as row_dend_reorder. row_order Order of rows. Manually setting row order turns off clustering. column_order Order of column. row_labels Optional row labels which are put as row names in the heatmap. row_names_side Should the row names be put on the left or right of the heatmap? show_row_names Whether show row names. row_names_max_width Maximum width of row names viewport. row_names_gp Graphic parameters for row names. row_names_rot Rotation of row names. row_names_centered Should row names put centered? column_labels Optional column labels which are put as column names in the heatmap. column_names_side Should the column names be put on the top or bottom of the heatmap? column_names_max_height Maximum height of column names viewport. show_column_names Whether show column names. column_names_gp Graphic parameters for drawing text. column_names_rot Rotation of column names. column_names_centered Should column names put centered? top_annotation A HeatmapAnnotation object. bottom_annotation A HeatmapAnnotation object. left_annotation It should be specified by rowAnnotation. right_annotation it should be specified by rowAnnotation. km Apply k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row slice, hierarchical clustering is still applied with parameters above. 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. row_km Same as km. row_km_repeats Number of k-means runs to get a consensus k-means clustering. Note if row_km_repeats is set to more than one, the final number of groups might be smaller than row_km, but this might means the original row_km is not a good choice. row_split Same as split. column_km K-means clustering on columns. column_km_repeats Number of k-means runs to get a consensus k-means clustering. Similar as row_km_repeats. column_split Split on columns. For heatmap splitting, please refer to https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-split . gap Gap between row slices if the heatmap is split by rows. The value should be a unit object. row_gap Same as gap. column_gap Gap between column slices. show_parent_dend_line When heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms? width Width of the heatmap body. height Height of the heatmap body. heatmap_width Width of the whole heatmap (including heatmap components) heatmap_height Height of the whole heatmap (including heatmap components). Check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#size-of-the-heatmap . show_heatmap_legend Whether show heatmap legend? heatmap_legend_param A list contains parameters for the heatmap legends. See color_mapping_legend,ColorMapping-method for all available parameters. use_raster Whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. If number of rows or columns is more than 2000, it is by default turned on. Note if cell_fun is set, use_raster is enforced to be FALSE. raster_device Graphic device which is used to generate the raster image. raster_quality A value larger than 1. raster_device_param A list of further parameters for the selected graphic device. For raster image support, please check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image . raster_resize_mat Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image? The value can be logical. If it is TRUE, mean is used to summarize the sub matrix which corresponds to a single pixel. The value can also be a summary function, e.g. max. raster_by_magick Whether to use image_resize to scale the image. raster_magick_filter Pass to filter argument of image_resize. A character scalar and all possible values are in filter_types. The default is "Lanczos". post_fun A function which will be executed after the heatmap list is drawn.

Value

a ComplexHeatmap object

saezlab/ligrec_decoupler documentation built on Aug. 10, 2024, 8:56 a.m.