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Heatmap

Source: R/visualizations.R
visualize.heatmap.Rd

Generate a heatmap for the data.

Usage

visualize.heatmap(
  dataSet,
  pkg = "pheatmap",
  cluster_cols = TRUE,
  cluster_rows = FALSE,
  show_colnames = TRUE,
  show_rownames = TRUE,
  show_pct_cols = FALSE,
  show_pct_rows = TRUE,
  show_pct_legend = TRUE,
  saveRes = TRUE
)

Arguments

dataSet

The 2d data set of data.

pkg

A string (default = "pheatmap") specifying the source package used to plot the heatmap. Two options: "pheatmap" and "ggplot2".

cluster_cols

A boolean (default = TRUE) determining if rows should be clustered or hclust object. This argument only works when pkg = "pheatmap".

cluster_rows

A boolean (default = FALSE) determining if columns should be clustered or hclust object. This argument only works when pkg = "pheatmap".

show_colnames

A boolean (default = TRUE) specifying if column names are be shown. This argument only works when pkg = "pheatmap".

show_rownames

A boolean (default = TRUE) specifying if row names are be shown. This argument only works when pkg = "pheatmap".

show_pct_cols

A boolean (default = FALSE) specifying whether to append the percentage of missing values to the column names. Only applied when dataSet contains missing values.

show_pct_rows

A boolean (default = TRUE) specifying whether to append the percentage of missing values to the row names. Only applied when dataSet contains missing values.

show_pct_legend

A boolean (default = TRUE) specifying whether the percentages of missing and present values in the entire dataset are shown in the legend. Only applied when dataSet contains missing values.

saveRes

A boolean (default = TRUE) specifying whether to save a summary of missingness information. Only applied when dataSet contains missing values.

Value

An object of class ggplot.

Details

A summary of missingness information including:

  • "count_missing_protein": The count of missing values for each protein.

  • "pct_missing_protein": The percentage of missing values for each protein.

  • "pct_missing_total": The percentage of missing values for each protein relative to the total missing values in the entire dataset.