DynamicPlot

Plot dynamic features across pseudotime.

Usage

DynamicPlot(
  srt,
  lineages,
  features,
  group.by = NULL,
  cells = NULL,
  layer = "counts",
  assay = NULL,
  family = NULL,
  exp_method = c("log1p", "raw", "zscore", "fc", "log2fc"),
  lib_normalize = identical(layer, "counts"),
  libsize = NULL,
  compare_lineages = TRUE,
  compare_features = FALSE,
  add_line = TRUE,
  add_interval = TRUE,
  line.size = 1,
  line_palette = "Dark2",
  line_palcolor = NULL,
  add_point = TRUE,
  pt.size = 1,
  point_palette = "Paired",
  point_palcolor = NULL,
  add_rug = TRUE,
  flip = FALSE,
  reverse = FALSE,
  x_order = c("value", "rank"),
  aspect.ratio = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list(),
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  seed = 11
)

Arguments

srt: A Seurat object.
lineages: A character vector specifying the lineages to plot.
features: A character vector specifying the features to plot.
group.by: A character specifying a metadata column to group the cells by. Default is NULL.
cells: A character vector specifying the cells to include in the plot. Default is NULL.
layer: A character string specifying the layer to use for the analysis. Default is "counts".
assay: A character string specifying the assay to use for the analysis. Default is NULL.
family: A character specifying the model used to calculate the dynamic features if needed. By default, this parameter is set to NULL, and the appropriate family will be automatically determined.
exp_method: A character specifying the method to transform the expression values. Default is "log1p" with options "log1p", "raw", "zscore", "fc", "log2fc".
lib_normalize: A boolean specifying whether to normalize the expression values using library size. Default the layer is counts, this parameter is set to TRUE. Otherwise, it is set to FALSE.
libsize: A numeric vector specifying the library size for each cell. Default is NULL.
compare_lineages: A boolean specifying whether to compare the lineages in the plot. Default is TRUE.
compare_features: A boolean specifying whether to compare the features in the plot. Default is FALSE.
add_line: A boolean specifying whether to add lines to the plot. Default is TRUE.
add_interval: A boolean specifying whether to add confidence intervals to the plot. Default is TRUE.
line.size: A numeric specifying the size of the lines. Default is 1.
line_palette: A character string specifying the name of the palette to use for the line colors. Default is "Dark2".
line_palcolor: A vector specifying the colors to use for the line palette. Default is NULL.
add_point: A boolean specifying whether to add points to the plot. Default is TRUE.
pt.size: A numeric specifying the size of the points. Default is 1.
point_palette: A character string specifying the name of the palette to use for the point colors. Default is "Paired".
point_palcolor: A vector specifying the colors to use for the point palette. Default is NULL.
add_rug: A boolean specifying whether to add rugs to the plot. Default is TRUE.
flip: A boolean specifying whether to flip the x-axis. Default is FALSE.
reverse: A boolean specifying whether to reverse the x-axis. Default is FALSE.
x_order: A character specifying the order of the x-axis values. Default is c("value", "rank").
aspect.ratio: A numeric specifying the aspect ratio of the plot. Default is NULL.
legend.position: A character string specifying the position of the legend in the plot. Default is "right".
legend.direction: A character string specifying the direction of the legend in the plot. Default is "vertical".
theme_use: A character string specifying the name of the theme to use for the plot. Default is "theme_scop".
theme_args: A list specifying the arguments to pass to the theme function. Default is list().
combine: A boolean specifying whether to combine multiple plots into a single plot. Default is TRUE.
nrow: A numeric specifying the number of rows in the combined plot. Default is NULL.
ncol: A numeric specifying the number of columns in the combined plot. Default is NULL.
byrow: A boolean specifying whether to fill plots by row in the combined plot. Default is TRUE.
seed: A numeric specifying the random seed. Default is 11.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- RunSlingshot(
  pancreas_sub,
  group.by = "SubCellType",
  reduction = "UMAP"
)

CellDimPlot(
  pancreas_sub,
  group.by = "SubCellType",
  reduction = "UMAP",
  lineages = paste0("Lineage", 1:2),
  lineages_span = 0.1
)

DynamicPlot(
  pancreas_sub,
  lineages = "Lineage1",
  features = c("Arxes1", "Ncoa2", "G2M_score"),
  group.by = "SubCellType",
  compare_features = TRUE
)

DynamicPlot(
  pancreas_sub,
  lineages = c("Lineage1", "Lineage2"),
  features = c("Arxes1", "Ncoa2", "G2M_score"),
  group.by = "SubCellType",
  compare_lineages = TRUE,
  compare_features = FALSE
)

DynamicPlot(
  pancreas_sub,
  lineages = c("Lineage1", "Lineage2"),
  features = c("Arxes1", "Ncoa2", "G2M_score"),
  group.by = "SubCellType",
  compare_lineages = FALSE,
  compare_features = FALSE
)
} # }

Usage

Arguments

See also

Examples