RepeatedHighDim (version 2.4.0)

scTC_trim_effect: scTC_trim_effect: Compare scTrimClust trimming against default Seurat analysis

Description

Visualizes the impact of scTrimClust's trimming by comparing gene sets between: 1) Default Seurat analysis (no trimming) 2) scTrimClust post-trimming results

Usage

scTC_trim_effect(
  method_pairs,
  method_colors,
  set_colors = setNames(c("#4D4D4D", "#AEAEAE", "#E6E6E6"), c("S1:standard",
    "S2:intersect", "S3:trimmed")),
  heatmap_color_palette = colorRamp2(seq(0, 100, 1), heat.colors(101, rev = TRUE)),
  column_title = "",
  row_names_side = "right",
  legend_name = "No. of\nmarkers",
  row_names_gp = 10,
  column_title_gp = 12
)

Value

A Heatmap object from the ComplexHeatmap package.

Arguments

method_pairs

A named list of method comparisons. Each element should be a list with two components (data1 (untrimmed) and data2 (trimmed)) containing data frames with:

• cluster: Cluster identifiers

• gene: Gene identifiers

method_colors

Named vector of colors for method annotations. Names should match the names in method_pairs.

set_colors

Named vector of colors for set annotations (S1-S3). Default: c("S1:standard", "S2:intersect", "S3:trimmed") with grey colors.

heatmap_color_palette

Color mapping function for heatmap. Default: colorRamp2(seq(0, 100, 1), heat.colors(101, rev = TRUE)).

column_title

Main title for the heatmap columns.

row_names_side

Side for row names ("left" or "right"). Default: "right".

legend_name

Title for the heatmap legend. Default: "No. of markers".

row_names_gp

Graphics parameters for row names. Default: 10.

column_title_gp

Graphics parameters for column title. Default: 12.

Details

scTC_trim_effect creates a heatmap showing the percentage differences in gene sets between method pairs across clusters. The heatmap shows three components for each method comparison:

• Column 1-3: Unique to method1 (untrimmed), Intersection, Unique to method2 (trimmed)

• Rows represent (cell) clusters with counts from first method in parentheses

• Columns are split by method pairs

Examples

if (FALSE) {

method_pairs <- list(
  CLR = list(
    data1 = RepeatedHighDim:::scTC_eff_clr,
    data2 = RepeatedHighDim:::scTC_eff_clr_robust
  ),
  LogNorm = list(
    data1 = RepeatedHighDim:::scTC_eff_log,
    data2 = RepeatedHighDim:::scTC_eff_log_robust
  )
)

method_colors <- setNames(grey.colors(2), c("CLR", "LogNorm"))

scTC_trim_effect(
  method_pairs = method_pairs,
  method_colors = method_colors,
  column_title = "nPCs:5, nFeatures:1000"
)

set_colors <- grey.colors(3)
names(set_colors) <- c("S1:standard", "S2:intersect", "S3:trimmed")

scTC_trim_effect(
  method_pairs = method_pairs,
  method_colors = method_colors,
  set_colors = setNames(c("blue", "green", "red"), names(set_colors)),
  heatmap_color_palette = colorRamp2(c(0, 50, 100), c("white", "pink", "purple")),
  column_title = "Custom Color Example"
)
}