Visualize as extended heatmap

Visualize the transcript proportions and additional annotation in a heatmap.

plot_proportion_pheatmap(
  dturtle,
  genes = NULL,
  sample_meta_table_columns = NULL,
  include_expression = FALSE,
  savepath = NULL,
  filename_ext = "_pheatmap.png",
  add_to_table = FALSE,
  BPPARAM = BiocParallel::SerialParam(),
  ...
)

Arguments

dturtle	dturtle result object of posthoc_and_stager().
genes	Character vector of genes to plot. If NULL, defaults to all found significant genes (sig_genes).
sample_meta_table_columns	Specify the columns of meta_table_sample that shall be used as column annotations. Defaults to all available columns. The first table column must match with the sample identifiers.
include_expression	Include gene expression as additional column annotation. Computes the log₂ of the expression values with a pseudocount of 1.
savepath	If you want your files to be saved to disk, specify a save path here. The directories will be created if necessary.
filename_ext	Optionally specify a file name extension here, which also defines the save image format. The file name will be 'gene_name+extension'.
add_to_table	If a savepath is provided, add the filepaths of the created plots to the corresponding entries in dtu_table. The name of the column that shall be created can be specified here.
BPPARAM	If multicore processing should be used, specify a BiocParallelParam object here. Among others, can be SerialParam() (default) for non-multicore processing or MulticoreParam('number_cores') for multicore processing. See BiocParallel for more information.
...	Arguments passed on to pheatmap::pheatmap mat numeric matrix of the values to be plotted. color vector of colors used in heatmap. kmeans_k the number of kmeans clusters to make, if we want to aggregate the rows before drawing heatmap. If NA then the rows are not aggregated. breaks a sequence of numbers that covers the range of values in mat and is one element longer than color vector. Used for mapping values to colors. Useful, if needed to map certain values to certain colors, to certain values. If value is NA then the breaks are calculated automatically. When breaks do not cover the range of values, then any value larger than max(breaks) will have the largest color and any value lower than min(breaks) will get the lowest color. border_color color of cell borders on heatmap, use NA if no border should be drawn. cellwidth individual cell width in points. If left as NA, then the values depend on the size of plotting window. cellheight individual cell height in points. If left as NA, then the values depend on the size of plotting window. scale character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none" cluster_rows boolean values determining if rows should be clustered or hclust object, cluster_cols boolean values determining if columns should be clustered or hclust object. clustering_distance_rows distance measure used in clustering rows. Possible values are "correlation" for Pearson correlation and all the distances supported by dist, such as "euclidean", etc. If the value is none of the above it is assumed that a distance matrix is provided. clustering_distance_cols distance measure used in clustering columns. Possible values the same as for clustering_distance_rows. clustering_method clustering method used. Accepts the same values as hclust. clustering_callback callback function to modify the clustering. Is called with two parameters: original hclust object and the matrix used for clustering. Must return a hclust object. cutree_rows number of clusters the rows are divided into, based on the hierarchical clustering (using cutree), if rows are not clustered, the argument is ignored cutree_cols similar to cutree_rows, but for columns treeheight_row the height of a tree for rows, if these are clustered. Default value 50 points. treeheight_col the height of a tree for columns, if these are clustered. Default value 50 points. legend logical to determine if legend should be drawn or not. legend_breaks vector of breakpoints for the legend. legend_labels vector of labels for the legend_breaks. annotation_row data frame that specifies the annotations shown on left side of the heatmap. Each row defines the features for a specific row. The rows in the data and in the annotation are matched using corresponding row names. Note that color schemes takes into account if variable is continuous or discrete. annotation_col similar to annotation_row, but for columns. annotation deprecated parameter that currently sets the annotation_col if it is missing annotation_colors list for specifying annotation_row and annotation_col track colors manually. It is possible to define the colors for only some of the features. Check examples for details. annotation_legend boolean value showing if the legend for annotation tracks should be drawn. annotation_names_row boolean value showing if the names for row annotation tracks should be drawn. annotation_names_col boolean value showing if the names for column annotation tracks should be drawn. drop_levels logical to determine if unused levels are also shown in the legend show_rownames boolean specifying if column names are be shown. show_colnames boolean specifying if column names are be shown. main the title of the plot fontsize base fontsize for the plot fontsize_row fontsize for rownames (Default: fontsize) fontsize_col fontsize for colnames (Default: fontsize) angle_col angle of the column labels, right now one can choose only from few predefined options (0, 45, 90, 270 and 315) display_numbers logical determining if the numeric values are also printed to the cells. If this is a matrix (with same dimensions as original matrix), the contents of the matrix are shown instead of original values. number_format format strings (C printf style) of the numbers shown in cells. For example "%.2f" shows 2 decimal places and "%.1e" shows exponential notation (see more in sprintf). number_color color of the text fontsize_number fontsize of the numbers displayed in cells gaps_row vector of row indices that show where to put gaps into heatmap. Used only if the rows are not clustered. See cutree_row to see how to introduce gaps to clustered rows. gaps_col similar to gaps_row, but for columns. labels_row custom labels for rows that are used instead of rownames. labels_col similar to labels_row, but for columns. filename file path where to save the picture. Filetype is decided by the extension in the path. Currently following formats are supported: png, pdf, tiff, bmp, jpeg. Even if the plot does not fit into the plotting window, the file size is calculated so that the plot would fit there, unless specified otherwise. width manual option for determining the output file width in inches. height manual option for determining the output file height in inches. silent do not draw the plot (useful when using the gtable output) na_col specify the color of the NA cell in the matrix.

Value

Returns list of saved plots, for adding to the DTU table. If no savepath is provided, returns a list of the created plots for further processing.

Details

Highly flexible visualization, relying on the pheatmap package.

See also

run_drimseq() and posthoc_and_stager() for DTU object creation. create_dtu_table() and plot_dtu_table() for table visualization.

Other DTUrtle visualization: create_dtu_table(), plot_dimensional_reduction(), plot_proportion_barplot(), plot_transcripts_view()