Run UMAP analysis and plot the results

hd_auto_umap() runs a UMAP analysis on the provided data and plots the UMAP results.

Usage

hd_auto_umap(
  dat,
  metadata = NULL,
  by_sample = TRUE,
  impute = TRUE,
  plot_x = "UMAP1",
  plot_y = "UMAP2",
  plot_color = NULL,
  plot_palette = NULL
)

Arguments

dat

An HDAnalyzeR object or a dataset in wide format and sample ID as its first column.

metadata

A dataset containing the metadata information with the sample ID as the first column. If a HDAnalyzeR object is provided, this parameter is not needed.

by_sample

If TRUE, points represent samples. If FALSE, points represent features. Default is TRUE.

impute

If TRUE, missing values will be imputed using the k-nearest neighbors algorithm (k = 5). Default is TRUE. description

plot_x

The name of the column in dim_res that contains the x-axis values. Default is "PC1".

plot_y

The name of the column in dim_res that contains the y-axis values. Default is "PC2".

plot_color

The name of the column in dim_res that contains the variable to be used to plot the points color. Default is NULL.

plot_palette

The color palette for the plot. If it is a character, it should be one of the palettes from hd_palettes(). Default is NULL.

Value

A list with the UMAP results and UMAP plots.

Examples

# Create the HDAnalyzeR object providing the data and metadata
hd_object <- hd_initialize(example_data, example_metadata)

# Run the UMAP analysis
hd_auto_umap(hd_object, plot_color = "Disease", plot_palette = "cancers12")
#> $umap_res
#> # A tibble: 586 × 3
#>    DAid     UMAP1  UMAP2
#>    <chr>    <dbl>  <dbl>
#>  1 DA00001 -2.62   0.384
#>  2 DA00002  1.99   1.73 
#>  3 DA00003 -1.69  -1.87 
#>  4 DA00004 -2.17  -1.74 
#>  5 DA00005 -2.83   0.315
#>  6 DA00006  1.54  -0.733
#>  7 DA00007 -3.49  -0.886
#>  8 DA00008  1.54  -1.08 
#>  9 DA00009 -0.655  0.278
#> 10 DA00010  1.93   1.53 
#> # ℹ 576 more rows
#> 
#> $by_sample
#> [1] TRUE
#> 
#> $umap_plot

#> 
#> attr(,"class")
#> [1] "hd_umap"