gene_featureplot: gene_featureplot Function

In PALMO: Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

gene_featureplot Function

Description

This function allows to output the user-defined input features expression in graphical format. Users can select x-axis as donor/participant (x_group_by='PTID') and expression on y-axis organized by variable time (var_oi='Time'). Add group facet feature like facet_by='celltype'.

Usage

gene_featureplot(
  data_object = NULL,
  data = NULL,
  anndata = NULL,
  featureList,
  x_group_by = "PTID",
  var_oi = "Time",
  xlab = "group_by",
  ylab = "Value/Expression",
  ncol = NULL,
  facet_by = NULL,
  compare_means = FALSE,
  x_text_angle = NULL,
  text_font = NULL
)

Arguments

data_object	Input PALMO S4 object. It contains annotation information and expression data from Bulk or single cell data.
data	Optional, Data can be bulk data or single cell data
anndata	Optional, Annotation dataframe consist of information such as Sample (sample name), PTID (donor/participant), Time (longitudinal timepoints)
featureList	User-defined feature or genelist as a vector
x_group_by	x-axis grouping variable like 'PTID'
var_oi	x-axis subgrouping variable like 'Time'
xlab	x-axis label
ylab	y-axis label
ncol	Number of columns in the plot grid
facet_by	A set of variables or expressions
compare_means	Add mean comparison p-value in a plot (for more information refer http://rpkgs.datanovia.com/ggpubr/reference/stat_compare_means.html)
x_text_angle	xaxis text angle on ggplot
text_font	font size on ggplot

Value

gene plot

Examples

## Not run: 
plots <- gene_featureplot(data_object=palmo_obj,
featureList=c('LILRA4', 'CLEC9A'))

## End(Not run)

PALMO documentation built on Aug. 18, 2022, 1:06 a.m.