Gene and ESTIMATE score relationship plots — EstimateGenePlot • scop

Compare ESTIMATE scores between target-gene high and low expression groups, or draw continuous gene-expression correlations with ESTIMATE scores.

Usage

EstimateGenePlot(
  object = NULL,
  score.data = NULL,
  gene.data = NULL,
  features,
  assay = NULL,
  layer = "data",
  plot_type = c("violin", "scatter"),
  split = c("median", "quantile"),
  quantile = 0.5,
  cor_method = c("spearman", "pearson", "kendall"),
  add_stat = TRUE,
  ...
)

Arguments

object: Optional RunESTIMATE() bundle, SummarizedExperiment, or Seurat object containing ESTIMATE results.
score.data: Optional score matrix or data frame with samples in rows.
gene.data: Optional gene expression matrix with genes in rows and samples in columns.
features: Target genes to plot.
assay: Assay used for `Seurat` or `SummarizedExperiment` expression.
layer: Assay layer used for `Seurat` expression.
plot_type: Plot type.
split: Split method for high/low groups in violin plots.
quantile: Quantile cutoff used when `split = "quantile"`.
cor_method: Correlation method for scatter plots.
add_stat: Whether to add group comparison labels to violin or box plots. Requires ggpubr.
...: Additional plotting arguments.

Value

A `ggplot` object.