Run UMAP analysis

do_umap() runs a UMAP analysis on the provided data. The function can visualize the sample points on the first and second UMAP plane. It can also save the plots in the results directory.

Usage

do_umap(
  olink_data,
  metadata = NULL,
  color = "Disease",
  palette = NULL,
  wide = TRUE,
  assay = FALSE,
  impute = TRUE,
  plots = TRUE,
  save = FALSE
)

Arguments

olink_data

A tibble with the data to be used in the UMAP analysis.

metadata

A tibble with metadata information to be used in the UMAP plots. Default is NULL.

color

The name of the column in metadata that contains the variable. to be used to plot the points color. Default is "Disease".

palette

A vector with the colors to be used in the UMAP plots. Default is NULL.

wide

If TRUE, the data is assumed to be in wide format. Default is TRUE.

assay

If TRUE, each point is an assay and not a sample. Default is FALSE.

impute

If TRUE, the data is imputed before the UMAP analysis. Default is TRUE.

plots

If TRUE, the function creates plots of the UMAP results. Default is TRUE.

save

If TRUE, the plots are saved in the results directory. Default is FALSE.

Value

A list with the UMAP results and, if requested, the UMAP plots.

• umap_res: A tibble with the UMAP results.

• umap_plot: A ggplot object with the data points on the 1st and 2nd UMAPs plane.

Examples

do_umap(example_data,
       metadata = example_metadata,
       wide = FALSE,
       color = "Sex",
       palette = "sex_hpa")
#> $umap_res
#> # A tibble: 586 × 3
#>    DAid     UMAP1   UMAP2
#>    <fct>    <dbl>   <dbl>
#>  1 DA00001 -2.39  -0.211 
#>  2 DA00002  1.42   2.15  
#>  3 DA00003 -1.07  -2.34  
#>  4 DA00004 -1.57  -2.31  
#>  5 DA00005 -2.71  -0.450 
#>  6 DA00006  1.88  -0.286 
#>  7 DA00007 -2.90  -1.75  
#>  8 DA00008 -0.300  1.73  
#>  9 DA00009 -0.803  0.0411
#> 10 DA00010  1.03   2.13  
#> # ℹ 576 more rows
#> 
#> $umap_plot

#>