trelli_rnaseq_nonzero_bar: Bar chart trelliscope building function for Non-Zero counts...

In pmartR/pmartRqc: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Bar chart trelliscope building function for Non-Zero counts in RNA-seq data

Description

Specify a plot design and cognostics for the Non-Zero barchart trelliscope. Non-Zeroes are displayed per panel_by variable. Main_effects data is used to split samples when applicable. For MS/NMR data, use "trelli missingness bar".

Usage

trelli_rnaseq_nonzero_bar(
  trelliData,
  cognostics = c("total count", "non-zero count", "non-zero proportion"),
  proportion = TRUE,
  ggplot_params = NULL,
  interactive = FALSE,
  path = .getDownloadsFolder(),
  name = "Trelliscope",
  test_mode = FALSE,
  test_example = 1,
  single_plot = FALSE,
  ...
)

Arguments

trelliData	A trelliscope data object made by as.trelliData.edata or as.trelliData. Must be built using seqData. Required.
cognostics	A vector of cognostic options for each plot. Defaults are "total count", "non-zero count", and "non-zero proportion". If grouping data is included, all cognostics will be reported per group. If the trelliData is paneled by a biomolecule, the counts and proportion we be samples. If paneled by a sample or biomolecule class, the counts and proportions will be biomolecules.
proportion	A logical to determine whether plots should display counts or proportions. Default is TRUE.
ggplot_params	An optional vector of strings of ggplot parameters to the backend ggplot function. For example, c("ylab(”)", "xlab(”)"). Default is NULL.
interactive	A logical argument indicating whether the plots should be interactive or not. Interactive plots are ggplots piped to ggplotly (for now). Default is FALSE.
path	The base directory of the trelliscope application. Default is Downloads.
name	The name of the display. Default is Trelliscope.
test_mode	A logical to return a smaller trelliscope to confirm plot and design. Default is FALSE.
test_example	A vector of plot indices to return for test_mode. Default is 1.
single_plot	A TRUE/FALSE to indicate whether 1 plot (not a trelliscope) should be returned. Default is FALSE.
...	Additional arguments to be passed on to the trelli builder

Value

No return value, builds a trelliscope display of bar charts that is stored in 'path'

Author(s)

David Degnan, Lisa Bramer

Examples

## Not run: 
library(pmartRdata)

trelliData_seq1 <- as.trelliData.edata(e_data = rnaseq_edata, 
                                      edata_cname = "Transcript",
                                      omics_type = "seqData")
omicsData_seq <- group_designation(omicsData = rnaseq_object, main_effects = c("Virus"))

# Filter low transcript counts
omicsData_seq <- applyFilt(filter_object = total_count_filter(omicsData = omicsData_seq), 
 omicsData = omicsData_seq, min_count = 15)

# Select a normalization and statistics method (options are 'edgeR', 'DESeq2', and 'voom').
# See ?difexp_seq for more details
statRes_seq <- diffexp_seq(omicsData = omicsData_seq, method = "voom")

# Generate the trelliData object
trelliData_seq2 <- as.trelliData(omicsData = omicsData_seq)
trelliData_seq3 <- as.trelliData(statRes = statRes_seq)
trelliData_seq4 <- as.trelliData(omicsData = omicsData_seq, statRes = statRes_seq)

# Build the non-zero bar plot with an edata file. Generate trelliData in as.trelliData.edata
trelli_panel_by(trelliData = trelliData_seq1, panel = "Transcript") %>% 
  trelli_rnaseq_nonzero_bar(test_mode = TRUE, test_example = 1:10, path = tempdir())
trelli_panel_by(trelliData = trelliData_seq1, panel = "Sample") %>% 
  trelli_rnaseq_nonzero_bar(test_mode = TRUE, test_example = 1:10, 
   cognostics = "non-zero proportion", path = tempdir())

# Build the non-zero bar plot with an omicsData object. Generate trelliData in as.trelliData
trelli_panel_by(trelliData = trelliData_seq2, panel = "Transcript") %>% 
  trelli_rnaseq_nonzero_bar(test_mode = TRUE, test_example = 1:10, path = tempdir())

# Build the non-zero bar plot with a statRes object. Generate trelliData in as.trelliData
trelli_panel_by(trelliData = trelliData_seq3, panel = "Transcript") %>%
  trelli_rnaseq_nonzero_bar(test_mode = TRUE, test_example = 1:10,
                         cognostics = c("non-zero proportion"), path = tempdir())

# Build the non-zero bar plot with an omicsData and statRes object. 
# Generate trelliData in as.trelliData.
trelli_panel_by(trelliData = trelliData_seq4, panel = "Gene") %>%
  trelli_rnaseq_nonzero_bar(test_mode = TRUE, test_example = 1:10, path = tempdir()) 

# Or making the plot interactive 
trelli_panel_by(trelliData = trelliData_seq2, panel = "Transcript") %>% 
   trelli_rnaseq_nonzero_bar(test_mode = TRUE, test_example = 1:5, 
     interactive = TRUE, path = tempdir())
   
# Or visualize only count data 
trelli_panel_by(trelliData = trelliData_seq2, panel = "Transcript") %>% 
   trelli_rnaseq_nonzero_bar(test_mode = TRUE, test_example = 1:5, 
     cognostics = "non-zero count", proportion = FALSE, path = tempdir())

\dontshow{closeAllConnections()}   

## End(Not run)

pmartR/pmartRqc documentation built on April 25, 2024, 6:18 a.m.