Compare scoring algorithms on a single signature via heatmap or boxplot.Source:
It may be useful to compare the results of scoring across several different
scoring algorithms via a method of visualization, such as a heatmap. The
compareSigs function allows the input of a SummarizedExperiment
data object and conducts
profiling on each signature desired, and outputting a heatmap or boxplot
for each signature.
compareAlgs( input, signatures = NULL, annotationColName, useAssay = "counts", algorithm = c("GSVA", "ssGSEA", "ASSIGN", "PLAGE", "Zscore", "singscore"), showColumnNames = TRUE, showRowNames = TRUE, scale = FALSE, colorSets = c("Set1", "Set2", "Set3", "Pastel1", "Pastel2", "Accent", "Dark2", "Paired"), choose_color = c("blue", "gray95", "red"), colList = list(), show.pb = FALSE, parallel.sz = 0, output = "heatmap", num.boot = 100, column_order = NULL )
an input data object of the class
listof signatures to run with their associated genes. This list should be in the same format as
TBsignatures, included in the TBSignatureProfiler package. If
signatures = NULL, the default set of signatures
TBsignatureslist is used. For details, run
?TBsignatures. If <2 genes in a signature are present in the sample, that signature will not be evaluated and will not be present in the resulting SE object. The default is
a character string giving the column name in
colDatathat contains the annotation data. Required.
a character string specifying the assay to use for signature profiling when
SummarizedExperiment. Required only for input data of the class
SummarizedExperiment. If null, the assay used will be
"counts". The default is
a vector of algorithms to run, or character string if only one is desired. The default is
c("GSVA", "ssGSEA", "ASSIGN", "PLAGE", "Zscore", "singscore").
showColumnNames = TRUEwill show the column names (i.e. sample names) on the heatmap. The default is
showColumnNames = TRUEwill show the row names (i.e. signature names) on the heatmap. The default is
scale = TRUEscales the signature data. The default is
a vector of names listing the color sets in the order that they should be used in creating the heatmap. By default, this function will use the color sets in the order listed in
Usagefor annotation information. You may replace the default with the same collection of sets in order that you want to use them, or provide custom color sets with the
a vector of color names to be interpolated for the heatmap gradient, or a
colorRampfunction produced by
circlize::colorRamp2. The default is
c("blue", "gray95", "red").
listof named vectors specifying custom color information to pass to
ComplexHeatmap::Heatmap(). The list should have as many elements as there are annotation columns, and each element name should correspond exactly with the name of each annotation column. The colors in the vector elements should be named according to the levels of the factor in that column's annotation data if the annotation is discrete, or it should be produced with
circlize::colorRamp2if the annotation is continuous. By default,
ColorBrewercolor sets will be used. See the the parameter
colorSetsfor additional details.
logical, whether warnings and other output from the profiling should be suppressed (including progress bar output). Default is
an integer identifying the number of processors to use when running the calculations in parallel for the GSVA and ssGSEA algorithms. If
parallel.sz = 0, all cores are used. The default is
a character string specifying whether the outputted plot should be a
"boxplot". The default is
an integer indicating the number of times to bootstrap the data.
a vector of character strings indicating the order in which to manually arrange the heatmap columns. Default is
NULL, such that column order is automatically determined via clustering.
compareAlgs(TB_indian, signatures = TBsignatures[c("Zimmer_RES_3")], annotationColName = "label", algorithm = c("ssGSEA", "PLAGE"), scale = TRUE, parallel.sz = 1, output = "heatmap") #> Parameter update_genes is TRUE. Gene names will be updated. #> Running ssGSEA #> Warning: 1 genes with constant expression values throuhgout the samples. #> Running PLAGE #> Warning: 1 genes with constant expression values throuhgout the samples. #> Warning: Since argument method!="ssgsea", genes with constant expression values are discarded.