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Analyze Data with Principal Component Analysis (PCA) for Cytokines.

Source: R/cyt_pca.R
cyt_pca.Rd

This function performs PCA on cytokine data and generates several types of plots: 2D individuals plot, optionally a 3D scatter plot (if style is "3d" and comp_num is 3), a scree plot, loadings plots for each component, a biplot (using the default stats::biplot), and a correlation circle plot.

Usage

cyt_pca(
  data,
  group_col = NULL,
  group_col2 = NULL,
  pca_colors = NULL,
  ellipse = FALSE,
  comp_num = 2,
  scale = NULL,
  pch_values = NULL,
  style = NULL,
  output_file = NULL,
  font_settings = NULL,
  progress = NULL,
  custom_fn = NULL
)

Arguments

data

A data frame containing cytokine data.

group_col

Character. The name of the column containing the grouping information.

group_col2

Character. The name of the second column containing the grouping information. If one is missing, the provided column is used for both.

pca_colors

A vector of pca_colors corresponding to the groups. If NULL, a palette is generated.

ellipse

Logical. If TRUE, a 95% confidence ellipse is drawn on the individuals plot.

comp_num

Numeric. Number of principal components to compute and display. Default is 2.

scale

Character. Optional transformation applied to numeric columns used in PCA. Supported values are NULL (default; no transformation), "none", "log2", "log10", "zscore", or "custom".

pch_values

A vector of plotting symbols.

style

Character. If "3d" (case insensitive) and comp_num equals 3, a 3D scatter plot is generated.

output_file

Optional. A file name for the PDF output. If NULL, interactive mode is assumed.

font_settings

Optional named list of font sizes for supported plot text elements.

progress

Optional. A Shiny Progress object for reporting progress updates.

custom_fn

Optional transformation function used when scale = "custom".

Value

In PDF mode, a PDF is created and the function returns NULL (invisibly). In interactive mode, a (possibly nested) list of recorded plots is returned.

Details

In PDF mode (if output_file or output_file is provided) the plots are printed to a PDF. In interactive mode (if both output_file and output_file are NULL) the plots are captured using recordPlot() and returned as a list for display in Shiny.

Author

Shubh Saraswat

Examples

data <- ExampleData1[, -c(3,23)]
data_df <- dplyr::filter(data, Group != "ND" & Treatment != "Unstimulated")
# Run PCA analysis and save plots to a PDF file
cyt_pca(
  data = data_df,
  output_file = NULL,
  pca_colors = c("black", "red2"),
  scale = "log2",
  comp_num = 3,
  pch_values = c(16, 4),
  style = "3D",
  group_col = "Group",
  group_col2 = "Treatment",
  ellipse = FALSE
)

#> $`CD3/CD28`
#> $`CD3/CD28`$overall_indiv_plot
#> 
#> $`CD3/CD28`$overall_3D
#> 
#> $`CD3/CD28`$overall_scree_plot
#> 
#> $`CD3/CD28`$loadings
#> $`CD3/CD28`$loadings[[1]]
#> 
#> $`CD3/CD28`$loadings[[2]]
#> 
#> $`CD3/CD28`$loadings[[3]]
#> 
#> 
#> $`CD3/CD28`$biplot
#> 
#> $`CD3/CD28`$correlation_circle
#> 
#> 
#> $LPS
#> $LPS$overall_indiv_plot
#> 
#> $LPS$overall_3D
#> 
#> $LPS$overall_scree_plot
#> 
#> $LPS$loadings
#> $LPS$loadings[[1]]
#> 
#> $LPS$loadings[[2]]
#> 
#> $LPS$loadings[[3]]
#> 
#> 
#> $LPS$biplot
#> 
#> $LPS$correlation_circle
#> 
#>