PALMO (version 0.1.2)

gene_featureplot: 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
)

Value

gene plot

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

Examples

if (FALSE) {
plots <- gene_featureplot(data_object=palmo_obj,
featureList=c('LILRA4', 'CLEC9A'))
}