Heatmap of DE results

Usage

plot_heatmap_DE(
  se,
  de_res,
  ain,
  comparison,
  condition = NULL,
  label_by = NULL,
  pvalue_column = "adj.P.Val",
  col_vector = NULL
)

Arguments

se: SummarizedExperiment containing all necessary information of the proteomics data set (including the normalized intensities)
de_res: data table resulting of run_DE
ain: Vector of strings of normalization methods to visualize (must be valid normalization methods saved in de_res)
comparison: String of comparison (must be a valid comparison saved in de_res)
condition: column name of condition (if NULL, condition saved in SummarizedExperiment will be taken)
label_by: String specifying the column to label the samples (If NULL, the labels column of the SummarizedExperiment object is used. If "No", no labeling of samples done.)
pvalue_column: column name of p-values in de_res
col_vector: Vector of colors to use for the heatmap. If NULL, default colors are used.

Value

list of ComplexHeatmaps for each method

Examples

data(tuberculosis_TMT_se)
data(tuberculosis_TMT_de_res)
plot_heatmap_DE(tuberculosis_TMT_se, tuberculosis_TMT_de_res, ain = NULL,
                comparison = "PTB-HC",
                condition = NULL, label_by = NULL,
                pvalue_column = "adj.P.Val", col_vector = NULL)
#> All assays of the SummarizedExperiment will be used.
#> Warning: raw: not valid normalization methods. Only valid normalization methods will be visualized.
#> Label of SummarizedExperiment used!
#> Condition of SummarizedExperiment used!
#> <simpleError in stats::hclust(stats::dist(as.matrix(data))): NA/NaN/Inf in foreign function call (arg 10)>
#> <simpleError in stats::hclust(stats::dist(as.matrix(data))): NA/NaN/Inf in foreign function call (arg 10)>
#> <simpleError in stats::hclust(stats::dist(as.matrix(data))): NA/NaN/Inf in foreign function call (arg 10)>
#> <simpleError in stats::hclust(stats::dist(as.matrix(data))): NA/NaN/Inf in foreign function call (arg 10)>
#> <simpleError in stats::hclust(stats::dist(as.matrix(data))): NA/NaN/Inf in foreign function call (arg 10)>
#> $log2

#> 
#> $RobNorm

#> 
#> $IRS_on_RobNorm

#> 
#> $Median

#> 
#> $IRS_on_Median

#>