Plot_Pseudotime_V_Gene_combo: Plot Violin Plots of Gene Expression by Group combo version
In eisascience/scCustFx: single-cell custom fxs Package

Plot_Pseudotime_V_Gene_combo

R Documentation

Plot Violin Plots of Gene Expression by Group combo version

Description

Plot Violin Plots of Gene Expression by Group combo version

Usage

Plot_Pseudotime_V_Gene_combo(
  SerObj,
  SerObjrtByName,
  Feats_pos = NULL,
  Feats_neg = NULL,
  base_size = 20,
  col_vector = col_vector,
  showScatter = TRUE,
  downsampleScatter = TRUE,
  scatterAlpha = 0.5,
  getWindows = T,
  decreasing = F,
  group.by = "Population"
)

Arguments

`SerObj`	A Seurat object containing the data to plot.
`Feats_pos`	The name of the feature to plot from pos side
`Feats_neg`	The name of the feature to plot from neg side
`getWindows`	Bool default T to get bins to split
`decreasing`	prder of pseudotime .
`group.by`	The name of the metadata field to group cells by.
`NumFeatName`	The name of the variable containing the number of features for each cell. If provided, cells with a number of features greater than the median will be excluded from the plot.
`cutGT`	If TRUE (default), cells with a number of features greater than the median will be excluded from the plot. If FALSE, cells with a number of features less than or equal to the median will be excluded from the plot.
`ThrCut`	The threshold for feature filtering. Cells with a value in the sdaCompName column greater than this threshold will be excluded from the plot. Default is 0, which will skip this step.
`GrpFacLevels`	The levels of the factor variable to use for grouping. If NULL (default), all levels will be included.
`compariSerObjns`	A list of compariSerObjns to perform using `stat_compare_means`. Each compariSerObjn should be a vector of two group names.
`xlab`	(Optional) The x-axis label.
`ylab`	(Optional) The y-axis label.
`palette`	The color palette to use for the plot.
`addJitter`	If TRUE, jitter points will be added to the plot. Default is FALSE.