validDIA: validDIA

In mgerault/DIAgui: A shiny app for processing DIAnn output in proteomics

validDIA

Description

Print plot showing proportion of non-missing values for each protein (or else) among the experiment

Usage

validDIA(
  data,
  transformation = c("none", "log2"),
  tit = "",
  data_type = c("intensity", "Top3", "iBAQ", "all"),
  design = NULL,
  to_check = NULL,
  prop_cut = 0.75
)

Arguments

data	Processed data from DIAnn (from iq processing or diann_matrix for example)
transformation	Which transformation do you want to apply (log2 or none)
tit	Title of your plot
data_type	The type of data you want to visualize; either 'intensity', 'Top3', 'iBAQ' or 'all'.
design	The design of your experiment that match your columns names. For example, if you have columns named '37_B1_Treatment', put c("temperature", "replicate", "condition"). If NULL, will take all values.
to_check	The grouping variable (same as in your design; like 'replicate' for example)
prop_cut	The minimum proportion to show on the graph

Details

If you have replicates or several conditions and you want to see the proportion of non-missing values for each replicate for example. Then, the id column in your data must be the first one; as in the output of the shiny app of DIAgui.

Value

ggplot2 graph showing proportion of non-missing values

mgerault/DIAgui documentation built on Nov. 7, 2024, 12:12 a.m.