inst/inlinehelp/foldchangeplot.md

In pinin4fjords/shinyngs: Shiny apps for NGS data

This page shows a simple scatter plot comparing the mean expression value between two groups of samples, for all rows of a matrix, plotted with Plotly [1].

Points are shown in grey, or blue if they match fold change and q value (where available) thresholds.

Controls

Expression matrix

Controls are provided to select with assay matrix, and which rows and columsn therein to use to contstruct the matrix to use in the plot.

Contrasts

The contrasts controls allow you to choose the comparison to be made, and the fold changes and q value threshold to use.

Scatter plot

This field group allows basic control on the size of the points, and whether the significant point are labelled (rarely a good idea).

Highlight points

It can often be useful to highlight sets of genes to illustrate trends. Use this set of filters to choose a set of genes to be highlighted by color on the plot.

References

• [1] Sievert C, Parmer C, Hocking T, Chamberlain S, Ram K, Corvellec M and Despouy P (2015). plotly: Create Interactive Web Graphics via Plotly's JavaScript Graphing Library. R package version 2.0.16, http://CRAN.R-project.org/package=plotly.

pinin4fjords/shinyngs documentation built on Feb. 28, 2024, 10:19 a.m.