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Create a density plot from the columns of a matrix

Source: R/plot-density2.R
plot_density2.Rd

This is an alternate to the plot_density() function using base graphics. The advantage of this function is that it should work with most matrix-like objects. This is especially helpful for DelayedArrays, which plot_density() does not handle.

Usage

plot_density2(
  x,
  metadata = NULL,
  col_by = NULL,
  hcl_palette = "Dark 3",
  plot_title = NULL,
  x_label = NULL,
  y_label = "Density",
  line_weight = 1,
  line_type = 1,
  show_legend = TRUE,
  legend_position = "topright",
  legend_horiz = FALSE,
  legend_cex = 0.8,
  legend_ncol = 1,
  ...
)

Arguments

x

feature x sample matrix or matrix-like object

metadata

data.frame containing metadata per sample. rownames of metadata must match the colnames of the input matrix. Default NULL, each sample in the matrix will be plotted.

col_by

metadata column used to color density lines. Default NULL, each sample in the matrix will be plotted.

hcl_palette

color palette applied to 'col_by' variable. One of the hcl.pals(). Default "Dark 3"

plot_title

title of the plot. Default NULL

x_label

x-axis title. Default NULL

y_label

y-axis title. Default "Density"

line_weight

line weight of the density lines. Default 1

line_type

line type of the density lines. Default 1

show_legend

should the legend be displayed on the plot if fill_by is set? Default TRUE

legend_position

location keyword for the legend. One of "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". Default "topright"

legend_horiz

logical; if TRUE, set the legend horizontally rather than vertically. Default FALSE

legend_cex

character expansion factor for legend text relative to current par. Default 0.8

legend_ncol

number of columns to set the legend items. Default 1. This is not used if legend_horiz=TRUE

...

Additional arguments not currently used.

Value

density plot of matrix columns

Examples


# Create metadata for plotting
metadata <- data.frame(row.names = colnames(GSE161650_lc))
metadata$Group <- rep(c("DMSO", "THZ1"), each = 3)

# Plot the density by sample
plot_density2(GSE161650_lc)


# Color each sample by their Group in metadata
plot_density2(
  GSE161650_lc,
  metadata,
  col_by = "Group",
  x_label = "log2 CPMs",
  plot_title = "Distribution of logCPM values"
  )