metacell-plots: Displays a correlation matrix of the quantitative data of a...

In samWieczorek/DAPAR2: Tools for the Differential Analysis of Proteins Abundance with R

Displays a correlation matrix of the quantitative data of a numeric matrix.

Description

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This method plots a bar plot which represents the distribution of the number of missing values (NA) per lines (ie proteins).

Plots a heatmap of the quantitative data. Each column represent one of the conditions in the object of class VizData and the color is proportional to the mean of intensity for each line of the dataset. The lines have been sorted in order to vizualize easily the different number of missing values. A white square is plotted for missing values.

#' Plots a heatmap of the quantitative data. Each column represent one of the conditions in the object of class MsnSet and the color is proportional to the mean of intensity for each line of the dataset. The lines have been sorted in order to vizualize easily the different number of missing values. A white square is plotted for missing values.

This method shows density plots which represents the repartition of Partial Observed Values for each replicate in the dataset. The colors correspond to the different conditions (slot Condition in in the dataset of class MsnSet). The x-axis represent the mean of intensity for one condition and one entity in the dataset (i. e. a protein) whereas the y-axis count the number of observed values for this entity and the considered condition.

Usage

mod_ds_metacell_ui(id)

mod_ds_metacell_server(
  id,
  vizData,
  pal = reactive({
     NULL
 }),
  pattern = reactive({
     NULL
 }),
  showSelect = reactive({
     TRUE
 })
)

metacellPerLinesHisto_HC(
  vizData,
  pattern = NULL,
  detailed = FALSE,
  indLegend = "auto",
  showValues = FALSE
)

metacellPerLinesHistoPerCondition_HC(
  vizData,
  pattern = NULL,
  indLegend = "auto",
  showValues = FALSE,
  pal = NULL
)

metacellHisto_HC(
  vizData,
  pattern = NULL,
  indLegend = "auto",
  showValues = FALSE,
  pal = NULL
)

wrapper.mvImage(vizData, pattern = "Missing MEC")

mvImage(vizData)

hc_mvTypePlot2(vizData, pal = NULL, pattern, typeofMV = NULL, title = NULL)

Arguments

id	xxx
vizData	xxx
pal	The different colors for conditions
pattern	xxx
showSelect	xxx
detailed	'value' or 'percent'
indLegend	xxx
showValues	A logical that indicates whether numeric values should be drawn above the bars.
typeofMV	xxx
title	The title of the plot

Value

NA

A bar plot

A heatmap

A heatmap

Density plots

Author(s)

Florence Combes, Samuel Wieczorek

Samuel Wieczorek, Alexia Dorffer

Samuel Wieczorek, Thomas Burger

Samuel Wieczorek

Examples

library(highcharter)
library(shinyBS)
library(shiny)

ui <- fluidPage(
  mod_ds_metacell_ui('test')
)

server <- function(input, output) {
  data(Exp1_R25_pept, package='DaparToolshedData')
  vList <- convert2viz(Exp1_R25_pept)
  vData <- [e-mail][[1]]
  
  rv <- reactiveValues(
    tags = NULL
  )
  #pattern <- c('Missing POV', 'Missing MEC')
   pattern <- NULL
   
  observe({
    rv$tags <- mod_ds_metacell_server('test',
                           vizData = reactive({vData}),
                           pal = reactive({NULL}),
                           pattern = reactive({pattern}),
                           showSelect = reactive({is.null(pattern)})
    )
  })
  
}

if (interactive())
  shinyApp(ui = ui, server = server)


library(QFeatures)
library(DaparViz)

#vList <- BuildExampleDataset('QFeatures')
vList <- BuildExampleDataset('MSnbase')
#vList <- BuildExampleDataset('list')

vData <- GetVizData(vList, 1)
pal <- ExtendPalette(length(unique(vData@conds)), "Dark2")


metacellPerLinesHisto_HC(vData, pattern = "Missing POV")
metacellPerLinesHisto_HC(vData)
metacellPerLinesHisto_HC(vData, pattern = "Quantified")
metacellPerLinesHisto_HC(vData, pattern = "Quant. by direct id")
metacellPerLinesHisto_HC(vData, pattern = "Quant. by recovery")
pattern <- c("Quantified", "Quant. by direct id", "Quant. by recovery")
metacellPerLinesHisto_HC(vData, pattern = pattern)


metacellPerLinesHistoPerCondition_HC(vData, pattern = "Missing POV")
metacellPerLinesHistoPerCondition_HC(vData)
metacellPerLinesHistoPerCondition_HC(vData, pattern = "Quantified")
metacellPerLinesHistoPerCondition_HC(vData, pattern = "Quant. by direct id")
metacellPerLinesHistoPerCondition_HC(vData, pattern = "Quant. by recovery")
pattern <- c("Quantified", "Quant. by direct id", "Quant. by recovery")
metacellPerLinesHistoPerCondition_HC(vData, pattern = pattern)


metacellHisto_HC(vData, pattern = "Missing POV")
metacellHisto_HC(vData)
metacellHisto_HC(vData, pattern = "Quantified")
metacellHisto_HC(vData, pattern = "Quant. by direct id")
metacellHisto_HC(vData, pattern = "Quant. by recovery")
pattern <- c("Quantified", "Quant. by direct id", "Quant. by recovery")
metacellHisto_HC(vData, pattern = pattern)
data(Exp1_R25_pept, package = 'DaparToolshedData')
vData <- convert2viz(Exp1_R25_pept)
pattern <- "Missing POV"
pal <- ExtendPalette(2, "Dark2")
metacellHisto_HC([e-mail][[1]], pattern, showValues = TRUE, pal = pal)

data(Exp1_R25_pept, package = 'DaparToolshedData')
vData <- convert2viz(Exp1_R25_pept)
mvImage([e-mail][[1]])

data(Exp1_R25_pept, package = 'DaparToolshedData')
vData <- convert2viz(Exp1_R25_pept)
pal <- ExtendPalette(length(unique([e-mail][[1]]@conds)), "Dark2")
pattern <- "Missing MEC"
hc_mvTypePlot2([e-mail][[1]], pattern = pattern, pal = pal)

samWieczorek/DAPAR2 documentation built on Oct. 15, 2023, 1:45 p.m.