scTC_bpplot: scTC_bpplot: Post-trim breakpoint heatmap for scTrimClust...

In RepeatedHighDim: Methods for High-Dimensional Repeated Measures Data

scTC_bpplot: Post-trim breakpoint heatmap for scTrimClust results

Description

Generates a heatmap showing the percentage overlap of marker genes between the original (untrimmed) cluster markers and markers identified after trimming at various percentages.

Usage

scTC_bpplot(
  ...,
  trim_percent_vector,
  plot_title = "scTrimClust: Post-trim Breakpoint Heatmap",
  legend_title = "Percent markes\nof non-trimmed",
  color = brewer.pal(n = 11, name = "RdYlBu")
)

Arguments

...	Two or more data.frames/tibbles containing marker genes from 'FindAllMarkers'.
trim_percent_vector	Numeric vector of trim percentages.
plot_title	Character string for the heatmap title.
legend_title	Character string for the legend title.
color	Color palette for the heatmap.

Details

scTC_bpplot compares marker genes between the original (untrimmed) clustering and trimmed versions. For each cluster, it calculates what percentage of the original markers are retained at each trim level. Clusters are ordered by the number of markers in the original (untrimmed) results.

At least two data.frames/tibbles containing marker genes from 'FindAllMarkers' (from the 'Seurat' package) should be provided to ... as input. The first data frame should be the original (untrimmed) results, followed by trimmed results.

trim_percent_vector must be a numeric vector of trim percentages corresponding to each input data frame (e.g., c(0,10,20,30,40) for untrimmed, 10 input data.frames/tibbles.

Value

A ComplexHeatmap object

Examples

## Not run: 
scTC_bpplot(
  covid_markers = RepeatedHighDim:::covid_markers,
  robust_covid_markers = RepeatedHighDim:::robust_covid_markers,
  robust_covid_markers_02trim = RepeatedHighDim:::robust_covid_markers_02trim,
  robust_covid_markers_03trim = RepeatedHighDim:::robust_covid_markers_03trim,
  robust_covid_data = RepeatedHighDim:::robust_covid_data,
  trim_percent_vector = c(0, 10, 20, 30, 40),
  plot_title = "CLR, nPCs:5, nFeatures:1000",
  legend_title = "Percent markers of non-trimmed"
)

## End(Not run)

RepeatedHighDim documentation built on April 15, 2025, 1:28 a.m.