Basic things you should know to use s-plot
This lists the basic information for using s-plot.
Currently supported plots
Please type s-plot.sh in command line directly to have the latest list.
#### Bars
./s-plot.sh barPlot
./s-plot.sh horizontalBar
./s-plot.sh multiBarNew
#### Lines
./s-plot.sh lines
./s-plot.sh lines.2
#### Dots
./s-plot.sh scatterplot
./s-plot.sh scatterplotColor
./s-plot.sh scatterplotContour
./s-plot.sh scatterplotLotsData
./s-plot.sh scatterplotMatrix
./s-plot.sh contourPlot (unfinished)
#### Distribution
./s-plot.sh areaplot
./s-plot.sh boxplot
./s-plot.sh densityPlot
./s-plot.sh densityHistPlot
./s-plot.sh histogram
./s-plot.sh histogram.2
#### Cluster
./s-plot.sh hcluster
./s-plot.sh hclust
#### Heatmap
./s-plot.sh heatmapS
./s-plot.sh heatmapM
./s-plot.sh heatmap.2
#### Others
./s-plot.sh volcano
./s-plot.sh vennDiagramBasic test data set
Here lists the general information of diamonds dataset that comes packaged with ggplot2.
This dataset contains ~50,000 entries. Each row is an individual diamond, and some of the variables of interest include the weight of the diamond in carats, color, clarity, and its price.
One can get, save and view the dataset using below commands. Or download data set from
> library(ggplot2)
> data(diamonds)
> head(diamonds)
carat cut color clarity depth table price x y z
1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43
2 0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31
3 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31
4 0.29 Premium I VS2 62.4 58 334 4.20 4.23 2.63
5 0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75
6 0.24 Very Good J VVS2 62.8 57 336 3.94 3.96 2.48
> summary(diamonds)
carat cut color clarity depth
Min. :0.2000 Fair : 1610 D: 6775 SI1 :13065 Min. :43.00
1st Qu.:0.4000 Good : 4906 E: 9797 VS2 :12258 1st Qu.:61.00
Median :0.7000 Very Good:12082 F: 9542 SI2 : 9194 Median :61.80
Mean :0.7979 Premium :13791 G:11292 VS1 : 8171 Mean :61.75
3rd Qu.:1.0400 Ideal :21551 H: 8304 VVS2 : 5066 3rd Qu.:62.50
Max. :5.0100 I: 5422 VVS1 : 3655 Max. :79.00
J: 2808 (Other): 2531
table price x y
Min. :43.00 Min. : 326 Min. : 0.000 Min. : 0.000
1st Qu.:56.00 1st Qu.: 950 1st Qu.: 4.710 1st Qu.: 4.720
Median :57.00 Median : 2401 Median : 5.700 Median : 5.710
Mean :57.46 Mean : 3933 Mean : 5.731 Mean : 5.735
3rd Qu.:59.00 3rd Qu.: 5324 3rd Qu.: 6.540 3rd Qu.: 6.540
Max. :95.00 Max. :18823 Max. :10.740 Max. :58.900
z
Min. : 0.000
1st Qu.: 2.910
Median : 3.530
Mean : 3.539
3rd Qu.: 4.040
Max. :31.800
#col.names=NA can generate an empty string to represent the name of first column
> write.table(diamonds, file="diamond.matrix",sep="\t", col.names=NA, row.names=T, quote=F)
#melt data set
> library(reshape2)
#Default all non-numerical column will be used as id variables
#melt will group each data value into combinations of factor variable or categorial variable.
> data_m <- melt(diamonds)
Using cut, color, clarity as id variables
> head(data_m)
cut color clarity variable value
1 Ideal E SI2 carat 0.23
2 Premium E SI1 carat 0.21
3 Good E VS1 carat 0.23
4 Premium I VS2 carat 0.29
5 Good J SI2 carat 0.31
6 Very Good J VVS2 carat 0.24
# Extract four columns from full data sets
> diamonds_extract <- diamonds[c(1,2,3,7)]
> diamonds_extract$price <- diamonds_extract$price / 1000
> head(diamonds_extract)
carat cut color price
1 0.23 Ideal E 0.326
2 0.21 Premium E 0.326
3 0.23 Good E 0.327
4 0.29 Premium I 0.334
5 0.31 Good J 0.335
6 0.24 Very Good J 0.336
> write.table(diamonds_extract, file="diamond.extract.matrix",sep="\t", col.names=NA, row.names=T, quote=F)
> diamonds_extract_melt <- melt(diamonds_extract)
Using cut, color as id variables
> head(diamonds_extract_melt)
cut color variable value
1 Ideal E carat 0.23
2 Premium E carat 0.21
3 Good E carat 0.23
4 Premium I carat 0.29
5 Good J carat 0.31
6 Very Good J carat 0.24
> tail(diamonds_extract_melt)
cut color variable value
107875 Premium D price 2.757
107876 Ideal D price 2.757
107877 Good D price 2.757
107878 Very Good D price 2.757
107879 Premium H price 2.757
107880 Ideal D price 2.757
> write.table(diamonds_extract_melt, file="diamond.extract.matrix.melt",sep="\t", row.names=F, quote=F)Basic layouts and themes
-
Legend position
Defult, the legend is posited at the right of pictures. One can give
topto-pto put the legend above pictures. Other accepted strings to-pisbottom,left,right, orc(0.008,0.8). The two element numerical vactor indicats the reltaive position of legend in pictures. 0.008 means position relative y-axis and 0.8 means position relative to x-axis. Specially,c(1,1)put legends at top-right. -
Width, Height, Resolution, type of output pictures
Default, width is
20 cm, one can givenumberto-wto change it. Height is12 cm, givenumberto-uto change height. Givenumberto-rto alter resolution instead of using300as default.8 picture formats are supported,
eps/ps,tex(pictex),pdf,jpeg,tiff,bmp,svgandwmf, withpngas default. Give any mentioned string to-Eto change output format. -
Title, xlab, ylab of picture
One can set title, xlab, ylab with
-t,-x,-y. -
Install modules
Give
TRUEto-ito install required modules for the first time. (iis shorted forinstall)Give
FALSEto-eif you only want to get the R scripts instead of running them. (eis shorted forexecute)
