Recent changes to visualization

visualization modified by Wei Li

Wei Li — Sun, 12 Apr 2020 21:33:54 -0000

--- v13
+++ v14
@@ -20,6 +20,8 @@
 Users can also modify the "Parameters" section in .Rmd file to adjust the parameters used in the report.

 An example of the generated html file (from test command) can be downloaded [here](https://sourceforge.net/projects/mageck/files/example/tim.report.nb.html/download).
+
+An example of the generated html file (from count command) can be downloaded [here](https://sourceforge.net/projects/mageck/files/example/tim_count.count_report.nb.html/download).

 Users need to install rmarkdown package as the dependency:

visualization modified by Wei Li

Wei Li — Sun, 12 Apr 2020 21:21:00 -0000

--- v12
+++ v13
@@ -6,7 +6,7 @@
 **The [MAGeCKFlute](https://www.bioconductor.org/packages/release/bioc/html/MAGeCKFlute.html) package provides a convenient approach to visualze MAGeCK and MAGeCK-VISPR results using R programming language.**

-**Visualization functions are also available within the MAGeCK software.** Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers.
+Visualization functions are also available within the MAGeCK software. Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers. **The in-house visualization module provides a simple solution for users with limited knowledge in R.**


 The Visualization function has additional software dependencies, but they are easy to install in many operating systems. See  [installation](https://sourceforge.net/p/mageck/wiki/install) for more details.

visualization modified by Wei Li

Wei Li — Sun, 12 Apr 2020 21:17:14 -0000

--- v11
+++ v12
@@ -19,6 +19,7 @@

 Users can also modify the "Parameters" section in .Rmd file to adjust the parameters used in the report.

+An example of the generated html file (from test command) can be downloaded [here](https://sourceforge.net/projects/mageck/files/example/tim.report.nb.html/download).

 Users need to install rmarkdown package as the dependency:

visualization modified by Wei Li

Wei Li — Sun, 12 Apr 2020 20:55:35 -0000

--- v10
+++ v11
@@ -3,20 +3,31 @@
 # Visualization Functions in MAGeCK #
 **We developed a stand-alone visualization tool, VISPR, to visualize CRISPR screening results. See the [paper](http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0843-6) and the [VISPR project](https://bitbucket.org/liulab/vispr) for more details.**

+**The [MAGeCKFlute](https://www.bioconductor.org/packages/release/bioc/html/MAGeCKFlute.html) package provides a convenient approach to visualze MAGeCK and MAGeCK-VISPR results using R programming language.**
+
+
 **Visualization functions are also available within the MAGeCK software.** Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers.
-
-An example of images generated by *plot* command:
-
-
-
-Here is another example of images generated by *count* command:
-
-


 The Visualization function has additional software dependencies, but they are easy to install in many operating systems. See  [installation](https://sourceforge.net/p/mageck/wiki/install) for more details.

-## The --pdf-report option ##
+## The R markdown option (since 0.5.9.3) ##
+
+Since 0.5.9.3, MAGeCK generates an R markdown file (.Rmd) for count and test options. Users can copy this file (along with all other files generated by MAGeCK) to a computer with [RStudio](https://rstudio.com/) installed, and generate a html based report page.
+
+To generate the report page, simply open the corresponding .Rmd file in RStudio, and press the "Run" --> "Run all" button. A html file will be generated correspondingly. 
+
+Users can also modify the "Parameters" section in .Rmd file to adjust the parameters used in the report.
+
+
+Users need to install rmarkdown package as the dependency:
+
+    install.packages("rmarkdown")
+
+
+## The --pdf-report option (before 0.5.9.3) ##
+
+**--pdf-report option will be gradually depreciated after version 0.5.9.3, due to its complicated dependencies on pdflatex.**

 MAGeCK will generate PDF files in both *count* and *test* command, by simply adding the *--pdf-report* option. If successful, a <prefix>.countsummary.pdf (for *count* command) or <prefix>_summary.pdf (for *test* command) will be generated. 

</prefix></prefix>

visualization modified by Wei Li

Wei Li — Fri, 22 Jul 2016 15:58:05 -0000

--- v9
+++ v10
@@ -3,7 +3,7 @@
 # Visualization Functions in MAGeCK #
 **We developed a stand-alone visualization tool, VISPR, to visualize CRISPR screening results. See the [paper](http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0843-6) and the [VISPR project](https://bitbucket.org/liulab/vispr) for more details.**

-**Visualization functions are also available with the MAGeCK software.** Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers.
+**Visualization functions are also available within the MAGeCK software.** Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers.

 An example of images generated by *plot* command:

visualization modified by Wei Li

Wei Li — Fri, 22 Jul 2016 15:57:49 -0000

--- v8
+++ v9
@@ -1,9 +1,9 @@
 [TOC]

 # Visualization Functions in MAGeCK #
-**We developed a stand-alone visualization tool, VISPR, to visualize CRISPR screening results. See the [paper](http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0843-6) and the [VISPR project](https://bitbucket.org/liulab/vispr) for more details.
+**We developed a stand-alone visualization tool, VISPR, to visualize CRISPR screening results. See the [paper](http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0843-6) and the [VISPR project](https://bitbucket.org/liulab/vispr) for more details.**

-Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers.
+**Visualization functions are also available with the MAGeCK software.** Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers.

 An example of images generated by *plot* command:

visualization modified by Wei Li

Wei Li — Fri, 22 Jul 2016 15:57:04 -0000

--- v7
+++ v8
@@ -1,6 +1,7 @@
 [TOC]

 # Visualization Functions in MAGeCK #
+**We developed a stand-alone visualization tool, VISPR, to visualize CRISPR screening results. See the [paper](http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0843-6) and the [VISPR project](https://bitbucket.org/liulab/vispr) for more details.

 Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers.

visualization modified by Wei Li

Wei Li — Mon, 27 Apr 2015 02:40:11 -0000

--- v6
+++ v7
@@ -2,9 +2,16 @@

 # Visualization Functions in MAGeCK #

-Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers:
+Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers.
+
+An example of images generated by *plot* command:

 
+
+Here is another example of images generated by *count* command:
+
+
+

 The Visualization function has additional software dependencies, but they are easy to install in many operating systems. See  [installation](https://sourceforge.net/p/mageck/wiki/install) for more details.

visualization modified by Wei Li

Wei Li — Mon, 27 Apr 2015 02:38:22 -0000

--- v5
+++ v6
@@ -4,7 +4,7 @@

 Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers:

-![The score of the MYC gene among the scores of all genes](http://a.fsdn.com/con/app/proj/mageck/screenshots/sample1_summary.png)
+

 The Visualization function has additional software dependencies, but they are easy to install in many operating systems. See  [installation](https://sourceforge.net/p/mageck/wiki/install) for more details.

visualization modified by Wei Li

Wei Li — Mon, 27 Apr 2015 02:34:34 -0000

--- v4
+++ v5
@@ -2,7 +2,9 @@

 # Visualization Functions in MAGeCK #

-Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers.
+Since version 0.5, MAGeCK enables a couple of visualization functions. With these features on, MAGeCK helps users better interpret datasets and results, and generates figures and tables that can be directly used in presentations or papers:
+
+![The score of the MYC gene among the scores of all genes](http://a.fsdn.com/con/app/proj/mageck/screenshots/sample1_summary.png)

 The Visualization function has additional software dependencies, but they are easy to install in many operating systems. See  [installation](https://sourceforge.net/p/mageck/wiki/install) for more details.