Bar plot of missing values per lines using highcharter

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 obj 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

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

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

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

wrapper.mvImage(obj, group = NULL, pattern = "Missing MEC")

mvImage(obj, group)

hc_mvTypePlot2(obj, group, pal = NULL, pattern, typeofMV = NULL, title = NULL)

Arguments

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

Value

A bar plot

A heatmap

Density plots

Author

Florence Combes, Samuel Wieczorek

Samuel Wieczorek, Alexia Dorffer

Samuel Wieczorek, Thomas Burger

Samuel Wieczorek

Examples

if (FALSE) { # interactive()
data(ft_na)
grp <- design.qf(ft_na)$Condition
metacellPerLinesHisto_HC(ft_na[[1]], group = grp, pattern = "Missing POV")
metacellPerLinesHisto_HC(ft_na[[1]])
metacellPerLinesHisto_HC(ft_na[[1]], group = grp, pattern = "Quantified")
metacellPerLinesHisto_HC(ft_na[[1]], group = grp, pattern = "Quant. by direct id")
metacellPerLinesHisto_HC(ft_na[[1]], group = grp, pattern = "Quant. by recovery")
pattern <- c("Quantified", "Quant. by direct id", "Quant. by recovery")
metacellPerLinesHisto_HC(ft_na[[1]], group = grp, pattern = pattern)


metacellPerLinesHistoPerCondition_HC(ft_na[[1]], group = grp, pattern = "Missing POV")
metacellPerLinesHistoPerCondition_HC(ft_na[[1]])
metacellPerLinesHistoPerCondition_HC(ft_na[[1]], group = grp, pattern = "Quantified")
metacellPerLinesHistoPerCondition_HC(ft_na[[1]], group = grp, pattern = "Quant. by direct id")
metacellPerLinesHistoPerCondition_HC(ft_na[[1]], group = grp, pattern = "Quant. by recovery")
pattern <- c("Quantified", "Quant. by direct id", "Quant. by recovery")
metacellPerLinesHistoPerCondition_HC(ft_na[[1]], group = grp, pattern = pattern)


metacellHisto_HC(ft_na[[1]], group = grp, pattern = "Missing POV")
metacellHisto_HC(ft_na[[1]])
metacellHisto_HC(ft_na[[1]], group = grp, pattern = "Quantified")
metacellHisto_HC(ft_na[[1]], group = grp, pattern = "Quant. by direct id")
metacellHisto_HC(ft_na[[1]], group = grp, pattern = "Quant. by recovery")
pattern <- c("Quantified", "Quant. by direct id", "Quant. by recovery")
metacellHisto_HC(ft_na[[1]], group = grp, pattern = pattern)


}
data(Exp1_R25_pept, package = 'DaparToolshedData')
pattern <- "Missing POV"
pal <- ExtendPalette(2, "Dark2")
metacellHisto_HC(Exp1_R25_pept[[1]], pattern, showValues = TRUE, pal = pal)
#> NULL

data(Exp1_R25_pept, package = 'DaparToolshedData')
mvImage(Exp1_R25_pept[[1]], design.qf(Exp1_R25_pept)$Condition)


data(Exp1_R25_pept, package = 'DaparToolshedData')
pal <- ExtendPalette(length(unique(design.qf(Exp1_R25_pept)$Condition)), "Dark2")
pattern <- "Missing MEC"
hc_mvTypePlot2(Exp1_R25_pept[[1]], group = design.qf(Exp1_R25_pept)$Condition, pattern = pattern, pal = pal)