plot_cnv {infercnv} | R Documentation

## Plot the matrix as a heatmap, with cells as rows and genes as columns, ordered according to chromosome

### Description

Formats the data and sends it for plotting.

### Usage

    plot_cnv(
      infercnv_obj,
      out_dir = ".",
      title = "inferCNV",
      obs_title = "Observations (Cells)",
      ref_title = "References (Cells)",
      cluster_by_groups = TRUE,
      cluster_references = TRUE,
      plot_chr_scale = FALSE,
      chr_lengths = NULL,
      k_obs_groups = 3,
      contig_cex = 1,
      x.center = mean(infercnv_obj@expr.data),
      x.range = "auto",
      hclust_method = "ward.D",
      custom_color_pal = NULL,
      color_safe_pal = FALSE,
      output_filename = "infercnv",
      output_format = "png",
      png_res = 300,
      dynamic_resize = 0,
      ref_contig = NULL,
      write_expr_matrix = FALSE,
      useRaster = TRUE
    )

### Arguments

`infercnv_obj` | infercnv object
`out_dir` | Directory in which to save pdf and other output.
`title` | Plot title.
`obs_title` | Title for the observations matrix.
`ref_title` | Title for the reference matrix.
`cluster_by_groups` | Whether to cluster observations by their annotations or not. Using this ignores k_obs_groups.
`cluster_references` | Whether to cluster references within their annotations or not. (dendrogram not displayed)
`plot_chr_scale` | Whether to scale the chromosme width on the heatmap based on their actual size rather than just the number of expressed genes.
`chr_lengths` | A named list of chromsomes lengths to use when plot_chr_scale=TRUE, or else chromosome size is assumed to be the last chromosome's stop position + 10k bp
`k_obs_groups` | Number of groups to break observation into.
`contig_cex` | Contig text size.
`x.center` | Value on which to center expression.
`x.range` | vector containing the extreme values in the heatmap (ie. c(-3,4) )
`hclust_method` | Clustering method to use for hclust.
`custom_color_pal` | Specify a custom set of colors for the heatmap. Has to be in the shape color.palette(c("darkblue", "white", "darkred"), c(2, 2))
`color_safe_pal` | Logical indication of using a color blindness safe palette.
`output_filename` | Filename to save the figure to.
`output_format` | format for heatmap image file (default: 'png'), options('png', 'pdf', NA) If set to NA, will print graphics natively
`png_res` | Resolution for png output.
`dynamic_resize` | Factor (>= 0) by which to scale the dynamic resize of the observation heatmap and the overall plot based on how many cells there are. Default is 0, which disables the scaling. Try 1 first if you want to enable.
`ref_contig` | If given, will focus cluster on only genes in this contig.
`write_expr_matrix` | Includes writing a matrix file containing the expression data that is plotted in the heatmap.
`useRaster` | Whether to use rasterization for drawing heatmap. Only disable if it produces an error as it is much faster than not using it.

### Value

A list of all relevent settings used for the plotting to be able to reuse them in another plot call while keeping consistant plotting settings, most importantly x.range.

### Examples

    # data(infercnv_data_example)
    # data(infercnv_annots_example)
    # data(infercnv_genes_example)

    # infercnv_object_example <- infercnv::CreateInfercnvObject(raw_counts_matrix=infercnv_data_example,
    #                                                           gene_order_file=infercnv_genes_example,
    #                                                           annotations_file=infercnv_annots_example,
    #                                                           ref_group_names=c("normal"))

    # infercnv_object_example <- infercnv::run(infercnv_object_example,
    #                                          cutoff=1,
    #                                          out_dir=tempfile(),
    #                                          cluster_by_groups=TRUE,
    #                                          denoise=TRUE,
    #                                          HMM=FALSE,
    #                                          num_threads=2,
    #                                          no_plot=TRUE)

    data(infercnv_object_example)

    plot_cnv(infercnv_object_example,
             out_dir=tempfile(),
             obs_title="Observations (Cells)",
             ref_title="References (Cells)",
             cluster_by_groups=TRUE,
             x.center=1,
             x.range="auto",
             hclust_method='ward.D',
             color_safe_pal=FALSE,
             output_filename="infercnv",
             output_format="png",
             png_res=300,
             dynamic_resize=0
             )

[Package infercnv version 1.10.1 Index]