git_R_STATS_KBS
RBioplot (former: frogplots) package for fully automated statistical analysis and data visualization.
It is awesome.
To cite in publication
Zhang J, Storey KB. (2016) RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistry. PeerJ 4:e2436.
Installation
-
Install devtools (if not already done)
install.packages("devtools") -
Install stable release
devtools::install_github("jzhangc/git_R_STATS_KBS/package/rbioplot") -
Install development build
devtools::install_github("jzhangc/git_R_STATS_KBS/package/rbioplot", ref = "beta")
Change Log
0.5.5 (5.10.2021)
- Updates to plotting functions
- All plotting functions now accepts data.frames
- rbioplot() now will automatically adjust figures for data only have one variable
0.5.4 (5.6.2021)
- General fix
- namespace updated with foreach pacakge
0.5.3 (11.11.2019)
- new functions to stats model
- rbiostats_normal(): stand-alone Shapiro-Wilk normality test function
- Updates to shiny apps
- rbioplot_app(): y_upper_limit now functional
- rbioplot_app(): colourpicker pacakge now imports updateColourInput function (due to: updateColourInput moved from Shiny to colourpicker)
0.5.2 (5.1.2018)
- multi_plot_shared_legend() added in preparation for multi-panel figure functionality: share one set of legend between multiple plots
- Shared functions added to the sharedfunctions.R file
0.5.1
- rightside y-axis now a seperate function: rightside_y()
- Bug fixes
0.5.0
- Shiny app interface overhaul with navigation bar at top
- Manual colour change added for rbioplot_app()
- Reset bar colour button added for rbioplot_app()
- Control panel items re-arranged for all shiny apps for a clearer presentation
- Output file suffix for rbioplot() and rbioplot_app() changed to ".bar.pdf"
- Bar graph outline colour customizable for rbioplot() via argument outlineCol
- Axes tick labels now can set as bold for the plotting functions via arguments xTickBold and yTickBold
- Axes tick labels now can set as bold for all plotting Shiny apps
- Intermediate function set_hue() added
- Bug fixes
0.4.3
- Font size for axis labels now customizable for all plotting functions via arguments xLabelSize, yLabelSize
- Font size for axis labels now customizable for all plotting Shiny apps
- Font size for axis title now customizable for all plotting functions vis argument TitleSize
- Font size for axis title now customizable for all plotting Shiny apps
- Font size for legend now customizable for all plotting functions via argument legendSize
- Font size for legend now customizable for all plotting Shiny apps
- Font size for legend title now customizable for all plotting functions via argument legendTtlSize
- Font size for legend title now customizable for all plotting Shiny apps
- Bar graph now can set as grey scale or automatic colour for rbioplot() via argument greyScale
- Bar graph now can set as grey scale or automatic colour for rbioplot_app()
- Bar graph outline colour customizable for rbioplot_app()
0.4.2
- Remote deployment concept for rbioplot_app() added
0.4.1
- The default position for plot titles set to "centre" for the web apps
- Typo fixes
- Bug fixes
0.4.0
- Web app version of the main functions added. To launch the app in the default web browser, run the corresponding app function (see below) in the R console:
- rbiostats_app()
- rbioplot_app()
- rbioplot_curve_app()
- rbioplot_heatmap_app()
- minor_tick() separeted from the main functions
- rbioplot(): errorbar label size now can be set via argument errorbarLblSize
- rbioplot_heatmap(): space between x-axis tick marks and the plot now can be set via arugment xSpace
- Bug fixes
0.3.8
- the case sensitive requirement for the “errorbar" argument of rbioplot(), rbioplot_curve(), autorange_bar_y() and autorange_curve() are now removed
- the case sensitive requirement for the “Tp" argument of rbiostats(), rbioplot() and rbioplot_heatmap() are now removed.
- display messages are added to rbiostats(), rbioplot(), rbioplot_curve() and rbioplot_heatmap()
- the suffix of the output file names has been changed:
- rbioplot(): .histogram.csv, .histogram.pdf
- rbioplot_curve(): .curve.csv, .curve.pdf
- rbioplot_heatmap(): .heatmap.csv, .heatmap.pdf
- editorial changes in documentation
- zzz.R file added
0.3.7
- rbioplot() now gives a proper error message if only one group (e.g. experimental condition) is present
- editorial changes in documentation
0.3.6
- Citation info added
0.3.5
- Bars now won't disappear for rbioplot() when the y-axis lower limit is set to a value other than zero.
- The distance between the errorbar label and errorbar now can be adjusted for rbioplot() through argument "errorbarLblSpace"
0.3.4
- Characters considered as special operators now can be included in the target names for the stats, histogram and heatmap modules, and will be displayed properly in the figures
- Users now can choose to avoid setting control to 1 for rbioplot() function, by setting "Nrm = FALSE”
- Users now can choose to display or hide the right side y-axis for histogram and curve modules by setting "rightsideY = TRUE" or "rightsideY = FALSE", respectively
- Bug fixes
0.3.3
- Backend updates for next feature update
0.3.1 - 0.3.2
- Bug fixes
0.3.0
- It is now possible to change the width of the errorbar with the argument errorbarWidth. Applicable functions: rbioplot(), rbioplot_curve()
- errorbarWidth: Set the width for errorbar. Defualt is 0.2
- it is now possible to change the size of the symbols for curve plots with the argument symbolSize. Applicable function: rbioplot_curve()
- symbolSize: Set the size of symbols. Default is 2
- It is now possible to hide the first column of the heatmap with the argument rmCntl. Applicable function: rbioplot_heatmap()
- rmCntl Remove the first column (i.e., control). Default is FALSE
- Bug fixes
0.2.5
- RBioplot now supports heatmap with the new function rbioplot_heatmap()
- Bug fixes
0.2.4
- It is now possible to use standard deviation (SD) as error bar via the new argument: errorbar. Functions with errorbar argument are: rbioplot(), rbioplot_curve(), autorange_bar_y(), autorange_curve()
- errorbar: Set the type of errorbar. Options are standard error of mean ("SEM"), or standard deviation ("SD"). Default is "SEM"
- It is now possible to change the font type for the graphs via the new argument: fontType. Functions with fontType argument are: rbioplot(), rbioplot_curve()
- fontType: The type of font in the figure. Default is "sans". For all options please refer to R font table, which is avaiable on the website: http://kenstoreylab.com/?page_id=69
- It is now possible to change the font size for ticks via the new arguments: xTickLblSize, yTickLblSize. Functions with fontType argument are: rbioplot(), rbioplot_curve()
- xTickLblSize: Font size of x axis ticks. Default is 10
- yTickLblSize: Font size of x axis ticks. Default is 10
- It is now possible to set tick font to italic via the new arguments: xTickItalic, yTickItalic. Functions with fontType argument are: rbioplot(), rbioplot_curve()
xTickItalic: Set x axis tick font to italic. Default is FALSE
yTickItalic: Set y axis tick font to italic. Default is FALSE
- Bug fixes
0.2.3
- The program has a new name: RBioplot. Along with the necessary name change for some functions, some minor new features have also been added to the existing functions
- Function name change (old -> new) *Note that the usage of those functions are unchanged*
- frogstats -> rbiostats
- frogplots -> rbioplot
- frogplots_curve -> rbioplot_cruve
- New features and changes
- rbioplot_curve():
- the function now detects the number of end numbers (i.e., if the data has replicates or not) and determines if error bar is needed for plotting
- the function now automatically assigns different line patterns for each experimental group
- autorange_curve(): consistent with the changes to rbioplot_curve, necessary adjustments have been made to make sure proper space management of the graph
- Bug fixes
- Other
The contact email address specific to the program is changed to jzhangcad@gmail.com. (Please note that this will not affect my current Gmail address, i.e., I am NOT switching my main email address to this)
0.2.2
- Bug fixes
0.2.1
- Bug fixes
0.2.0
- New functions:
- frogplots_curve(): A simple to use function for plotting joining-point curves with continuous x and y axises values
- autorange_bar_y(): A function to get custom lower/upper limit, major tick range, as well as minor tick options for y axis, based on a user-defined major tick number.
- autorange_curve(): A function to get custom lower/upper limit, major tick range, as well as minor tick options for both axises of a joint-piont curve with continuous x AND y values, based on a user-defined major tick number
- nat_dvsr(): A simple to use function to find all divisors for an integer number
- all_dvsr(): A function to find all divisors for any types of number
- Changes to existing functions:
- frogstats():
- Bartlett test has been added to test if the data have equal variance among groups - p > 0.05 means the variance is equal. Joining the S-W normality test, the Bartlett test is a default test that will be conducted regardless of the stats test type. Make sure the data meet the equal variance criterion as both conventional t-test and ANOVA (with all the post-hoc tests) assume the data is (1) normally distributed and (2) have equal variance. The results are included in the output .txt file
- t-test has been adjusted to “student’s t-test” (from “Welch's t-test”) to accurately reflect the equal variance aspect
- frogplots():
- New arguments have added to allow user-defined y axis range, y axis major tick range and minor tick patterns:
- y_custom_tick_range: To initiate setting the custom y_upper_limit, y_lower_limit, y_major_tick_range, y_n_minor_ticks. Default is FALSE
- y_lower_limit: Can only be set when y_custom_tick_range = TRUE. Set custom lower limt for y axis. Default is 0. Value can be obtained from the new function autorange_bar_y
- y_upper_limit: Can only be set when y_custom_tick_range = TRUE. Set custom upper limt for y axis. Value can be obtained from the new function autorange_bar_y
- y_major_tick_range: Can only be set when y_custom_tick_range = TRUE. Set custom major tick range for y axis. Value can be obtained from the new function autorange_bar_y
- y_n_minor_ticks: Can only be set when y_custom_tick_range = TRUE. Set custom numbers of minor ticks. Default is 4. Value can be obtained from the new function autorange_bar_y
- t-test within the function has been adjusted to “student’s t-test” from “Welch t-test” to reflect equal variance requirement
- Plot and axis titles are now bold by default.
- Small fixes, etc
- Bug fixes
0.1.0
- Initial commit