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https://github.com/rosscm/multigiviewer

:flashlight: Interactive R Shiny web application built with the {golem} framework to view multi-screen genetic interaction data
https://github.com/rosscm/multigiviewer

golem shiny

Last synced: about 2 months ago
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:flashlight: Interactive R Shiny web application built with the {golem} framework to view multi-screen genetic interaction data

Host: GitHub
URL: https://github.com/rosscm/multigiviewer
Owner: rosscm
License: other
Created: 2021-04-04T06:51:17.000Z (almost 4 years ago)
Default Branch: main
Last Pushed: 2021-06-30T18:04:35.000Z (over 3 years ago)
Last Synced: 2024-11-29T21:56:40.921Z (about 2 months ago)
Topics: golem, shiny
Language: R
Homepage: https://crispr.ccbr.utoronto.ca/crisprdb/
Size: 4.08 MB
Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.Rmd
- License: LICENSE

Awesome Lists containing this project

README

        ---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```



# multiGIviewer

An interactive R {shiny} web application built with the {golem} framework to view

multi-screen genetic interaction data



# Contents

- [Usage](#usage)

- [Inputs](#inputs)

- [Outputs](#outputs)

# Usage

Watch this short demo on how to use `multiGIviewer` to view replicated genetic

interactions (qGI scores) across two or more CRISPR screens of interest.

![](inst/demo.gif)

# Inputs

| Parameters              | Values     | Properties |

| ----------------------- | ---------- | ---------- |

| **Dataset**             | GIN_20210406, GIN_20210107, GIN_20201129, CHEM_20210218, CHEM_20210218_GIN_20210406 | qGI scores for 280 (GIN_20210406), 257 (GIN_20210107), 247 (GIN_20201129), 68 (CHEM_20210218), 348 (CHEM_20210218) & (GIN_20210406) screens [*required*; default GIN_20210406]

| **Screens**             | screens IDs | list of all screens in selected dataset; two or more screens need to be selected to view replicated interactions [*required*]

| **Media conditions(s)** | min, rich, pyro and/or DMSO | media type used to define wildtype single mutant fitness; more than one can be selected if screens were done in different media types [*required*]

| **FDR threshold**       | value from 0 to 1 | threshold to define significant genetic interactions; interactions must pass threshold in at least two screens to be shown [*required*; default 0.2]

| **Positive colour**     | HEX colour codes | colour to fill darkest positive points [*optional*; default `#FAE057`]

| **Negative colour**     | HEX colour codes | colour to fill darkest negative points [*optional*; default `#61C2FA`]

| **Plot labels**         | gene symbols | comma separated (character sensitive) list of genes to label on plot [*optional*; default top ten positive and negative interactions]

| **Label type**          | Text or Padded box | method to draw plot labels; padded box wraps text in a white box to better visualize labels [*optional*; default Text]

| **Reference line(s)**   | y=x, x=0 and/or y=0 | selection of reference lines to draw on plot [*optional*]

# Outputs

#### Plot

| Elements                                    | Properties |

| ---------------------------------------     | ---------- |

| **Fitness HAP1 wildtype [LFC] (x-axis)**    | corresponds to `mean_wtLFC` column

| **Fitness HAP1 knockout [LFC] (y-axis)**    | corresponds to `mean_koLFC` column

| **Genetic interaction in n screens (fill)** | corresponds to `n_sig` column

| **Mean qGI score (size)**                   | corresponds to `mean_qGI` column

#### Table

| Columns        | Properties |

| -------------- | ---------- |

| **gene**       | gene interaction

| **mean_qGI**   | mean qGI score of interaction across selected screens

| **min_FDR**    | minimum qGI FDR value of interaction across selected screens

| **mean_wtLFC** | mean wildtype dropout effect (log2-foldchange) across selected media condition(s)

| **mean_koLFC** | mean knockout dropout effect (log2-foldchange) across selected screens

| **n_sig**      | number of times positive or negative interaction is significant across selected screens

| **screen_sig** | list of screens where interaction is significant