Advanced Heatmap Visualization

Usage

jggheatmap(
  data,
  matrix_vars,
  row_var = NULL,
  col_var = NULL,
  value_var = NULL,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  clustering_method = "complete",
  distance_method = "euclidean",
  scaling = "none",
  color_scheme = "blue_red",
  cell_shape = "square",
  show_values = FALSE,
  value_format = "auto",
  text_size = 8,
  show_row_labels = TRUE,
  show_col_labels = TRUE,
  row_label_size = 10,
  col_label_size = 10,
  show_dendrograms = TRUE,
  dendrogram_height = 0.2,
  annotation_var = NULL,
  annotation_colors = "default",
  plot_title = "",
  plot_width = 600,
  plot_height = 600,
  show_colorbar = TRUE,
  colorbar_title = "Value",
  border_color = "white",
  na_color = "grey90",
  output_format = "plot_only"
)

Arguments

data: .
matrix_vars: Variables to include in the heatmap matrix
row_var: Variable defining row groupings (for pivot format)
col_var: Variable defining column groupings (for pivot format)
value_var: Variable containing matrix values (for pivot format)
cluster_rows: Perform hierarchical clustering on rows
cluster_cols: Perform hierarchical clustering on columns
clustering_method: .
distance_method: .
scaling: .
color_scheme: .
cell_shape: .
show_values: Display numeric values in cells
value_format: .
text_size: Size of text in cells
show_row_labels: .
show_col_labels: .
row_label_size: .
col_label_size: .
show_dendrograms: Display clustering dendrograms
dendrogram_height: Height of dendrogram relative to plot
annotation_var: Variable for row/column annotations
annotation_colors: .
plot_title: .
plot_width: .
plot_height: .
show_colorbar: Display color scale legend
colorbar_title: .
border_color: .
na_color: .
output_format: .

Value

A results object containing:

`results$plot`					an image
`results$matrixtab`					a table
`results$clustertab`					a table
`results$interpretation`					a html

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$matrixtab$asDF

as.data.frame(results$matrixtab)