dot-plotHeatmap: Prepare data for heatmaps and plot them

.plotHeatmapR Documentation

Prepare data for heatmaps and plot them

Description

Prepare data for heatmaps and plot them

Usage

.plotHeatmap(
  input,
  log_base_pval,
  ylimUp,
  FCcutoff,
  sig,
  clustering,
  numProtein,
  colorkey,
  width,
  height,
  log_base_FC,
  x.axis.size,
  y.axis.size,
  address,
  isPlotly
)

Arguments

input

data.table

log_base_pval

log base for p-values

ylimUp

for all three plots, upper limit for y-axis. FALSE (default) for volcano plot/heatmap use maximum of -log2 (adjusted p-value) or -log10 (adjusted p-value). FALSE (default) for comparison plot uses maximum of log-fold change + CI.

FCcutoff

for volcano plot or heatmap, whether involve fold change cutoff or not. FALSE (default) means no fold change cutoff is applied for significance analysis. FCcutoff = specific value means specific fold change cutoff is applied.

sig

FDR cutoff for the adjusted p-values in heatmap and volcano plot. level of significance for comparison plot. 100(1-sig)% confidence interval will be drawn. sig=0.05 is default.

clustering

Determines how to order proteins and comparisons. Hierarchical cluster analysis with Ward method(minimum variance) is performed. 'protein' means that protein dendrogram is computed and reordered based on protein means (the order of row is changed). 'comparison' means comparison dendrogram is computed and reordered based on comparison means (the order of comparison is changed). 'both' means to reorder both protein and comparison. Default is 'protein'.

numProtein

For ggplot2: The number of proteins which will be presented in each heatmap. Default is 100. Maximum possible number of protein for one heatmap is 180. For Plotly: use this parameter to adjust the number of proteins to be displayed on the heatmap

colorkey

TRUE(default) shows colorkey.

width

width of the saved file. Default is 10.

height

height of the saved file. Default is 10.

log_base_FC

log base for log-fold changes - 2 or 10

x.axis.size

size of axes labels, e.g. name of the comparisons in heatmap, and in comparison plot. Default is 10.

y.axis.size

size of axes labels, e.g. name of targeted proteins in heatmap. Default is 10.

address

the name of folder that will store the results. Default folder is the current working directory. The other assigned folder has to be existed under the current working directory. An output pdf file is automatically created with the default name of "VolcanoPlot.pdf" or "Heatmap.pdf" or "ComparisonPlot.pdf". The command address can help to specify where to store the file as well as how to modify the beginning of the file name. If address=FALSE, plot will be not saved as pdf file but showed in window.

isPlotly

This parameter is for MSstatsShiny application for plotly render, this cannot be used for saving PDF files as plotly do not have suppprt for PDFs currently. address and isPlotly cannot be set as TRUE at the same time.


MeenaChoi/MSstats documentation built on July 13, 2024, 10:59 a.m.