In rosscm/multiGIviewer: Multi-screen genetic interaction viewer
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.
# 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
rosscm/multiGIviewer documentation built on Dec. 22, 2021, 6:17 p.m.
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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.
# 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
rosscm/multiGIviewer documentation built on Dec. 22, 2021, 6:17 p.m.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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