R Histogram -- EndMemo

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R Histogram Plot Example

Histogram is a popular descriptive statistical method that shows data by dividing the range of values into intervals and plotting the frequency/density per interval as a bar.

hist(x, breaks = "Sturges", freq = NULL, ...)

x: value vector
breaks: number of bars
...

Following is a csv file example "histogram.csv", we will draw a Histogram of "Expression" values:

Subtype Expression A -0.54 A -0.8 A -1.03 A -0.41 A -1.31 A -0.66 A -0.43 A 1.01 A -1.15 A 0.14 A 1.42 A -0.3 A -0.16 A 0.15 A -0.62 A -0.42 A -0.4 A -0.35 A -0.42 A 0.32 A -0.57 A -0.07 A -0.06 A -0.24 A 0.02 A -0.39 A -0.74 A -0.92 A -0.09 A -0.03 A 0.18 A 0.25 A 0.48 A -0.39 A -0.24 A -0.3 A 0.25 A -0.42 A 0.54 A 0.03 A -0.66 A 0.3 A -0.38 A -0.03 A -0.62 A 0.14 A -1.68 A -0.77 A -0.8 A -0.09 A -0.8 A -0.41 A -0.88 A -0.27 A -0.55 A -0.07 A -1.6 A -0.11 A -0.79 A -0.33 A -1.26 A 1.31 A -0.33 A -0.43 A -0.92 A -0.11 A -0.29 A -1.02 A 0.41 A -0.81 A 0.61 A -0.63 A -0.49 A 0.18 A 0.17 A 0.24 A 0.13 A -0.12 A -0.24 A -0.26 A 1.48 A 0.04 A 0.81 A -0.56 A -1.12 A -0.19 A 0.27 A -1.28 A -0.38 A -0.83 A 0.25 A -0.14 A 0.45 A 0.29 A 0.18 A 0.74 A 0.44 A -0.28 A -0.31 A 0.08 A -0.18 A -0.29 A -0.62 A -0.08 A -0.87 A 0.19 A 0.54 A 0.34 A 0.54 A -0.35 A 0.02 A -0.39 A 0.38 A 1.25 A -0.51 A -0.39 A 0.05 A -0.36 A -0.19 A -1.49 A -0.1 A 0.08 A -1.16 A -0.77 A 1.58 A -0.92 A 0.59 A -0.35 A 0.26 A -0.78 A 1.2 A 0.06 A -0.68 A -0.19 A -0.44 A 0.56 A 0.93 A -0.35 A 0.11 A -0.22 A -0.12 A -0.22 A 0.29 B -0.67 B -0.77 B -0.03 B -0.12 B -0.57 B -0.76 B 0.19 B -1.8 B 0.35 B -0.81 B 1.8 B -0.99 B -2.22 B -1.06 B -0.69 B 0.06 B -0.2 B -1.68 B -0.64 B -0.44 B 0.29 B -0.13 B -1.98 B -0.84 B 0.44 B 0 B -1.32 B -0.54 B -0.05 B -0.54 B 0.23 B 0.38 B 0.35 B -0.61 B 0.3 B -0.33 B 0.79 B -1.39 B -0.06 B -0.88 B 0.44 B 0.32 B -0.45 B 0.21 B 0.2 B -2.03 B 0.59 B -0.78 B -0.92 B -0.96 B -0.1 B -0.07 B 0.39 B -0.39 B -1.11 B -0.98 B -0.11 B -1.78 B -0.73 B -1.01 B -0.5 B -0.16 B -0.59 B -1.46 B 1.13 B 1.01 B 1 B 0.21 B -0.21 B -1.05 B -1.34 B -0.72 B -0.47 B 0.1 B 0.15 C 1.67 C 0.81 C -1.81 C -1.18 C 0.49 C -1.74 C -1.57 C 0.46 C 1.31 C 0.16 C -0.39 C -0.4 C 0.44 C 1.18 C -2.08 C -1.62 C -0.3 C -1.53 C 0.03 C -0.42 C -1.91 C -1.86 C -1.99 C -0.25 C -1.14 C -2.11 C -0.93 C 0.42 C -1.13 C 0.13 C -0.92 C -0.34 C 0.38 C -2.01 C 1.42 C 0.1 C -0.44 C -2.17 C 0.13 C -1.75 C 0.52 C -1.18 C 0.85 C 1.11 C 0.64 C 0.97 C -0.72 C -0.04 C 0.38 C -1.87 C -0.89 C -2.09 C -1.54 C -0.17 C 0.09 C -0.25 C 0.51 C 0.33 C -1.29 C -0.51 C -1.62 C -0.5 C -0.52

Let first read in the data from the file:

>x <- read.csv("histogram.csv",header=T,sep="\t")
>x <- t(x)
>ex <- as.numeric(x[2,1:ncol(x)])

Plot a histogram:

>hist(ex)

The above plot is just a basic histogram. Let's add some parameters:

•br=20, #divide the data into 20 bars
•col="blue", #fill in blue color
•main="Histogram of Expression", #title of the histogram
•xlab="Expression", #x axis description
•ylab="Frequency", #y axis description
•freq=TRUE, #y axis is the frequency of each interval

Here is the command:

>hist(ex,br=14,col="blue",xlab="Expression",ylab="Frequency",
+freq=TRUE,main="Histogram of Expression")

To add a density line into the histogram, we need to change two parameters:

•freq=FALSE, #y axis is the density value of each interval
•ylab="Density", #y axis description as Density

Here is the command:

>hist(ex,br=14,col="blue",xlab="Expression",ylab="Density",freq=FALSE,
+main="Histogram of Expression")
>lines(density(ex),col="red")

We can write the plot into a file:

>png("histogram3.png",400,300)
>hist(ex,br=14,col="blue",xlab="Expression",ylab="Density",
+freq=FALSE,main="Histogram of Expression")
>lines(density(ex),col="red")
>graphics.off()

List of hist(...) parameters:

hist(x, ...) hist(x, breaks = "Sturges", freq = NULL, probability = !freq, include.lowest = TRUE, right = TRUE, density = NULL, angle = 45, col = NULL, border = NULL, main = paste("Histogram of" , xname), xlim = range(breaks), ylim = NULL, xlab = xname, ylab, axes = TRUE, plot = TRUE, labels = FALSE, nclass = NULL, warn.unused = TRUE, ...) Arguments: x: a vector of values for which the histogram is desired. breaks: one of: . a vector giving the breakpoints between histogram cells, . a single number giving the number of cells for the histogram, . a character string naming an algorithm to compute the number of cells . a function to compute the number of cells. In the last three cases the number is a suggestion only. freq: logical; if 'TRUE', the histogram graphic is a representation of frequencies, the 'counts' component of the result; if 'FALSE', probability densities, component 'density', are plotted (so that the histogram has a total area of one). Defaults to 'TRUE' _if and only if_ 'breaks' are equidistant (and 'probability' is not specified). probability: an _alias_ for '!freq', for S compatibility. include.lowest: logical; if 'TRUE', an 'x[i]' equal to the 'breaks' value will be included in the first (or last, for 'right = FALSE') bar. This will be ignored (with a warning) unless 'breaks' is a vector. right: logical; if 'TRUE', the histogram cells are right-closed (left open) intervals. density: the density of shading lines, in lines per inch. The default value of 'NULL' means that no shading lines are drawn. Non-positive values of 'density' also inhibit the drawing of shading lines. angle: the slope of shading lines, given as an angle in degrees (counter-clockwise). col: a colour to be used to fill the bars. The default of 'NULL' yields unfilled bars. border: the color of the border around the bars. The default is to use the standard foreground color. main, xlab, ylab: these arguments to 'title' have useful defaults here. xlim, ylim: the range of x and y values with sensible defaults. Note that 'xlim' is _not_ used to define the histogram (breaks), but only for plotting (when 'plot = TRUE'). axes: logical. If 'TRUE' (default), axes are draw if the plot is drawn. plot: logical. If 'TRUE' (default), a histogram is plotted, otherwise a list of breaks and counts is returned. In the latter case, a warning is used if (typically graphical) arguments are specified that only apply to the 'plot = TRUE' case. labels: logical or character. Additionally draw labels on top of bars, if not 'FALSE' nclass: numeric (integer). For S(-PLUS) compatibility only, 'nclass' is equivalent to 'breaks' for a scalar or character argument. warn.unused: logical. If 'plot=FALSE' and 'warn.unused=TRUE', a warning will be issued when graphical parameters are passed to 'hist.default()'. ...: further arguments and graphical parameters passed to 'plot.histogram' and thence to 'title' and 'axis' (if 'plot=TRUE').

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