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