Description Usage Arguments Value References
Plot data summary statistics in terms of the proportion of variance explained.
1 2 3 4 5 6 7 8 | plotVarExplained(
data,
posF = TRUE,
binarize = FALSE,
core = MulticoreParam(),
pathTitle = "GO pathways",
fileName = NULL
)
|
data |
The input dataset (either data.frame or matrix). Rows are the samples, columns are the probes/genes, except that the first column is the label (the outcome). |
posF |
A logical value indicating if only positively outcome-associated features should be used. (Default: TRUE) |
binarize |
A logical value indicating if the individual features under investigation should be binarized. The default is FALSE, which provides the estimated class probabilities for each pathway-level feature. If TRUE, then the binary output is given for each feature. |
core |
The number of cores used for computation. (Default: 1) |
pathTitle |
A string indicating the name of pathway under investigation. This will be displayed as the name of y-axis. |
fileName |
The file name specified for the plot. If it is not NULL, then the plot will be generated. The plot will project the data on the first two components. (Default: 'R2explained.png') |
An output image file with '.png' format.
Yu, Guangchuang, et al. 'clusterProfiler: an R package for comparing biological themes among gene clusters.' Omics: a journal of integrative biology 16.5 (2012): 284-287.
Perlich, C., & Swirszcz, G. (2011). On cross-validation and stacking: Building seemingly predictive models on random data. ACM SIGKDD Explorations Newsletter, 12(2), 11-15.
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