projectScoreLandscape: Project data on the landscape plot obtained from...
In singscore: Rank-based single-sample gene set scoring method

Description Usage Arguments Value See Also

This function takes the output (ggplot object) of the function plotScoreLandscape() and a new dataset. It projects the new data points onto the landscape plot and returns a new ggplot object with projected data points.

projectScoreLandscape(
  plotObj = NULL,
  scoredf1,
  scoredf2,
  annot = NULL,
  annot_name = NULL,
  subSamples = NULL,
  sampleLabels = NULL,
  isInteractive = FALSE
)

`plotObj`	a ggplot object, resulted from `plotScoreLandscape()`
`scoredf1`	data.frame, result of the simpleScore() function which scores the gene expression matrix against a gene set of interest
`scoredf2`	data.frame, result of the simpleScore() function which scores the gene expression matrix against another gene set of interest. Scores in scoredf1 and scoredf2 consist of the new data points that will be projected on the `plotObj` landscape plot.
`annot`	any numeric, character or factor annotation provided by the user that needs to be plot. Alternatively, this can be a character specifying the column of scoredf1 holding the annotation. Annotations must be ordered in the same way as the scores
`annot_name`	character, legend title for the annotation
`subSamples`	vector of character or indices for subsetting the scoredfs, default as NULL and all samples in scoredfs will be plotted. The subsetted samples are projected onto the landscape plot of `plotObj`.
`sampleLabels`	vector of character, sample names to display, ordered in the same way as samples are ordered in the 'scoredfs' data.frames and with labels for all samples. Samples whose labels should not be displayed should be left as empty strings or NAs. Default as NULL which means the projected points are not labelled.
`isInteractive`	boolean, whether the plot is interactive default as FALSE

New data points on the already plotted ggplot object from plotScoreLanscape()

plotScoreLandscape() @examples ranked <- rankGenes(toy_expr_se) scoredf1 <- simpleScore(ranked, upSet = toy_gs_up, downSet = toy_gs_dn) scoredf2 <- simpleScore(ranked, upSet = toy_gs_up) psl <- plotScoreLandscape(scoredf1, scoredf2) projectScoreLandscape(psl,scoredf1, scoredf2)

singscore documentation built on Nov. 8, 2020, 8:27 p.m.