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Heatmap visualization

Usage

viz_heatmap(
  data,
  metadata_info = NULL,
  metadata_sample = NULL,
  metadata_feature = NULL,
  plot_name = "",
  scale = "row",
  save_plot = "svg",
  enforce_featurenames = FALSE,
  enforce_samplenames = FALSE,
  print_plot = TRUE,
  path = NULL
)

Arguments

data

DF with unique sample identifiers as row names and metabolite numerical values in columns with metabolite identifiers as column names. Includes experimental design and outlier column.

metadata_info

Optional: NULL or Named vector where you can include vectors or lists for annotation c(individual_Metab= "ColumnName_metadata_feature",individual_Sample= "ColumnName_metadata_sample", color_Metab="ColumnName_metadata_feature", color_Sample= list("ColumnName_metadata_sample", "ColumnName_metadata_sample",...)).Default = NULL

metadata_sample

DF which contains information about the samples, which will be combined with your input data based on the unique sample identifiers. and other columns with required plot_typeInfo.Default = NULL

metadata_feature

Optional: DF with column "Metabolite" including the Metabolite names (needs to match Metabolite names of Input_data) and other columns with required plot_typeInfo. Default = NULL

plot_name

Optional: String which is added to the output files of the plot

scale

Optional: String with the information for scale row, column or none. Default = row

save_plot

Optional: Select the file type of output plots. Options are svg, pdf, png or NULL. Default = "svg"

enforce_featurenames

Optional: If there are more than 100 features no rownames will be shown, which is due to readability. You can Enforce this by setting this parameter to TRUE. Default = FALSE

enforce_samplenames

Optional: If there are more than 50 sampless no colnames will be shown, which is due to readability. You can Enforce this by setting this parameter to TRUE. Default = FALSE

print_plot

Optional: print the plots to the active graphic device.

path

Optional: String which is added to the resulting folder name default: NULL

Value

List with two elements: Plot and Plot_Sized

Examples

Intra <- intracell_raw%>%tibble::column_to_rownames("Code")
Res <- MetaProViz::viz_heatmap(data=Intra[,-c(1:3)])