Plot Number of Cells/Nuclei per Sample — CellBender_Diff

Plot of total cell or nuclei number per sample grouped by another meta data variable.

CellBender_Diff_Plot(
  feature_diff_df,
  pct_diff_threshold = 25,
  num_features = NULL,
  label = TRUE,
  num_labels = 20,
  min_count_label = 1,
  repel = TRUE,
  custom_labels = NULL,
  plot_line = TRUE,
  plot_title = "Raw Counts vs. Cell Bender Counts",
  x_axis_label = "Raw Data Counts",
  y_axis_label = "Cell Bender Counts",
  xnudge = 0,
  ynudge = 0,
  max.overlaps = 100,
  label_color = "dodgerblue",
  fontface = "bold",
  label_size = 3.88,
  bg.color = "white",
  bg.r = 0.15,
  ...
)

Arguments

feature_diff_df: name of data.frame created using CellBender_Feature_Diff.
pct_diff_threshold: threshold to use for feature plotting. Resulting plot will only contain features which exhibit percent change >= value. Default is 25.
num_features: Number of features to plot. Will ignore pct_diff_threshold and return plot with specified number of features. Default is NULL.
label: logical, whether or not to label the features that have largest percent difference between raw and CellBender counts (Default is TRUE).
num_labels: Number of features to label if label = TRUE, (default is 20).
min_count_label: Minimum number of raw counts per feature necessary to be included in plot labels (default is 1)
repel: logical, whether to use geom_text_repel to create a nicely-repelled labels; this is slow when a lot of points are being plotted. If using repel, set xnudge and ynudge to 0, (Default is TRUE).
custom_labels: A custom set of features to label instead of the features most different between raw and CellBender counts.
plot_line: logical, whether to plot diagonal line with slope = 1 (Default is TRUE).
plot_title: Plot title.
x_axis_label: Label for x axis.
y_axis_label: Label for y axis.
xnudge: Amount to nudge X and Y coordinates of labels by.
ynudge: Amount to nudge X and Y coordinates of labels by.
max.overlaps: passed to geom_text_repel, exclude text labels that overlap too many things. Defaults to 100.
label_color: Color to use for text labels.
fontface: font face to use for text labels (“plain”, “bold”, “italic”, “bold.italic”) (Default is "bold").
label_size: text size for feature labels (passed to geom_text_repel).
bg.color: color to use for shadow/outline of text labels (passed to geom_text_repel) (Default is white).
bg.r: radius to use for shadow/outline of text labels (passed to geom_text_repel) (Default is 0.15).
...: Extra parameters passed to geom_text_repel through LabelPoints.

Value

A ggplot object

Examples

if (FALSE) {
# get cell bender differences data.frame
cb_stats <- CellBender_Feature_Diff(seurat_object - obj, raw_assay = "RAW",
cell_bender_assay = "RNA")

# plot
CellBender_Diff_Plot(feature_diff_df = cb_stats, pct_diff_threshold = 25)
}