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 = "Zissou",
plot_title = NULL,
x_label = "",
y_label = "Density",
legend_position = "topright",
line_weight = 1,
line_type = 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 "Zissou"- plot_title
title of the plot. Default NULL
- x_label
x-axis title. Default ""
- y_label
y-axis title. Default "Density"
- legend_position
location keyword for the legend. One of "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". Default "topright"
- line_weight
line weight of the density lines. Default 1
- line_type
line type of the density lines. Default 1
- ...
Additional arguments not currently used.
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"
)
