Land Plot Drawing
Plots In Tamil Meaning
Plots Means In Bengali

In this article, we’ll describe how to plot easily means or medians with error bars. We’ll use ggplot2 based helper functions available in the ggpubr R package.

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Contents:

Prerequisites

Prerequisites

Required R package

You need to install the R package ggpubr, to easily create ggplot2-based publication ready plots.

Land Plot Drawing

We recommend to install the latest developmental version from GitHub as follow:

If the installation from Github failed, then try to install from CRAN as follow:

Load ggpubr:

Demo data sets

Data: ToothGrowth and mtcars data sets.

Error plots

R function: ggerrorplot() [in ggpubr].

Simplified format:

data: a data frame
x, y: x and y variables for plotting
desc_stat: descriptive statistics to be used for visualizing errors. Default value is “mean_se”. Allowed values are one of , “mean”, “mean_se”, “mean_sd”, “mean_ci”, “mean_range”, “median”, “median_iqr”, “median_mad”, “median_range”

For example, the following R code uses the ToothGrowth data set and plots y = “len” by x = “dose”.

It’s also possible to add jitter points (representing individual points), dot plots and violin plots:

To add p-values comparing means, use this:

Read more at : Add P-values and Significance Levels to ggplots.

Color by a grouping variable:

Line plots

You can create a line plot of mean +/- error using the function ggline()[in ggpubr]. The format is as follow:

Color by groups:

Bar plots

R function ggbarplot()[in ggpubr]. The format is as follow:

Color by groups:

Add labels

In this section we’ll plot group means with individual information.

Data: mtcars.

Create a bar plot with individual labels.

Application to gene expression data

In our previous article - Facilitating Exploratory Data Visualization: Application to TCGA Genomic Data - we described how to visualize gene expression data using box plots, violin plots, dot plots and stripcharts. We also demonstrated how to combine the plot of multiples variables (genes) in the same plot.

Plots In Tamil Meaning

Here we provide some R code to visualize the mean expression profile of one or multiple genes. We’ll use the gene expression data set described in our previous tutorial: Facilitating Exploratory Data Visualization: Application to TCGA Genomic Data.

The data set contains the mRNA expression for five genes of interest - GATA3, PTEN, XBP1, ESR1 and MUC1 - from 3 different data sets:

Breast invasive carcinoma (BRCA),
Ovarian serous cystadenocarcinoma (OV) and
Lung squamous cell carcinoma (LUSC)

The R code below displays the mean expression of three genes - “GATA3”, “PTEN” and “XBP1”.

You can also add other geometries on the mean plot such as jitter points, dotplot or violin. To add a violin plot, type this:

Plots Means In Bengali

To add jitter points, we’ll use a small subset of data for readability:

As previously shown, you can merge the three plots as follow:

Show line labels:

Let’s plot a complex plot with point labels:

Plot a bar plot of means:

Error plots: