Scatterplot for Gene Expression Values

Source: R/draw_scatterplot.R

[Experimental]

This produces a scatterplot of two genes or gene signatures.

draw_scatterplot(
  object,
  assay_name,
  x_spec,
  y_spec,
  color_var = NULL,
  facet_var = NULL,
  smooth_method = c("lm", "loess", "none")
)

Arguments

object

(AnyHermesData)
input.

assay_name

(string)
selects assay from input.

x_spec

(GeneSpec)
gene specification for the x-axis.

y_spec

(GeneSpec)
gene specification for the y-axis.

color_var

(string or NULL)
optional color variable, taken from input sample variables.

facet_var

(string or NULL)
optional faceting variable, taken from input sample variables.

smooth_method

(string)
smoothing method to use, either linear regression line (lm), local polynomial regression (loess) or none.

Value

The ggplot scatterplot.

Examples

object <- hermes_data
g <- genes(object)

draw_scatterplot(
  object,
  assay_name = "counts",
  facet_var = NULL,
  x_spec = gene_spec(c(A = g[1])),
  y_spec = gene_spec(g[2]),
  color = "RACE"
)


object2 <- object %>%
  add_quality_flags() %>%
  filter() %>%
  normalize()
g2 <- genes(object2)

draw_scatterplot(
  object2,
  assay_name = "tpm",
  facet_var = "SEX",
  x_spec = gene_spec(g2[1:10], colMeans, "Mean"),
  y_spec = gene_spec(g2[11:20], colMedians, "Median"),
  smooth_method = "loess"
)