modified boxplot and pheatmap, new rFunction script

README.md

@@ -1,5 +1,6 @@
 ### s-plot
-=====
+---
+
 A simple plot library based on `bash`, `R` mainly `ggplot2` to make
 the plot easily and flexibly.
 
@@ -18,11 +19,13 @@ ${filename} colorBar
 
 #### Lines
 ${filename} lines
+${filename} lines_lm
 
 #### Dots
 ${filename} pca
 ${filename} scatterplot
 ${filename} scatterplot2
+${filename} scatterplot3d
 ${filename} scatterplotColor
 ${filename} scatterplotContour
 ${filename} scatterplotLotsData
@@ -33,6 +36,7 @@ ${filename} contourPlot
 #### Distribution
 ${filename} areaplot
 ${filename} boxplot
+${filename} density2d
 ${filename} densityPlot
 ${filename} densityHistPlot
 ${filename} histogram
@@ -48,11 +52,20 @@ ${filename} heatmapM
 ${filename} heatmap.2
 ${filename} pheatmap
 ${filename} pretteyHeatmap
+${filename} areaplot.new
+
+### ecrichplot
+${filename} enrichmentPlot
 
 #### Others
 ${filename} volcano
 ${filename} vennDiagram
 ${filename} upsetView
+
+and other tools:
+${filename} png2eps
+${filename} boxplot.statistics
+${filename} colorLegend
 ```
 
 #### Basic test data set

error.txt

@@ -0,0 +1 @@
+sp_pheatmap:参数-G 丢失

example/areaplot/areaplot.data

@@ -0,0 +1,7 @@
+len	known_unexpr	known_expr	new	group
+30	1	0	0	1
+42	1	0	0	1
+45	3	0	0	1
+46	1	0	0	1
+48	2	0	0	1
+49	1	0	0	1

example/barplot/barplot.melt.data

@@ -0,0 +1,21 @@
+Pos	variable	value	Set	
+-5000	h3k27ac	8.71298
+-4000	h3k27ac	8.43246
+-3000	h3k27ac	8.25497
+-2000	h3k27ac	7.16265
+-1000	h3k27ac	3.55341
+0	h3k27ac	3.55030
+1000	h3k27ac	7.07502
+2000	h3k27ac	8.24328
+3000	h3k27ac	8.43869
+4000	h3k27ac	8.48877
+-5000	ctcf	10.69130
+-4000	ctcf	10.76680
+-3000	ctcf	10.54410
+-2000	ctcf	10.86350
+-1000	ctcf	8.45751
+0	ctcf	8.50316
+1000	ctcf	10.91430
+2000	ctcf	10.70220
+3000	ctcf	10.41010
+4000	ctcf	10.57570

example/barplot/barplot.normal.data

@@ -0,0 +1,11 @@
+Pos	h3k27ac	ctcf	enhancer	h3k4me3	polII
+-5000	8.71298	10.69130	11.7359	10.02510	8.26866
+-4000	8.43246	10.76680	11.8442	9.76927	7.78358
+-3000	8.25497	10.54410	12.2470	9.40346	6.96859
+-2000	7.16265	10.86350	12.6889	8.35070	4.84365
+-1000	3.55341	8.45751	12.8372	4.84680	1.26110
+0	3.55030	8.50316	13.4152	5.17401	1.50022
+1000	7.07502	10.91430	12.3588	8.13909	4.88096
+2000	8.24328	10.70220	12.3888	9.47255	7.67968
+3000	8.43869	10.41010	11.9760	9.80665	7.94148
+4000	8.48877	10.57570	11.6562	9.71986	8.17849

example/boxplot.statistics/boxplot.statistics.data

@@ -0,0 +1,9 @@
+Gene	hmC	expr	Set
+NM_001003918_26622	0	83.1269257376101	TP16
+NM_001011535_3260	0	0	TP16
+NM_001012640_14264	0	0	TP16
+NM_001012640_30427	0	0	TP16
+NM_001003918_2662217393_30486	0	0	TP16
+NM_001017393_30504	0	0	TP16
+NM_001025241_30464	0	0	TP16
+NM_001017393_30504001025241_30513	0	0	TP16

example/boxplot.statistics/boxplot.statistics.melt.data

@@ -0,0 +1,5 @@
+value	variable	Set
+0	hmC	g
+1	expr	g
+2	hmC	a
+3	expr	a

example/boxplot/boxplot.matrix2.data

@@ -0,0 +1,9 @@
+Gene	hmC	expr	Set
+NM_001003918_26622	0	83.1269257376101	TP16
+NM_001011535_3260	0	0	TP16
+NM_001012640_14264	0	0	TP16
+NM_001012640_30427	0	0	TP16
+NM_001003918_2662217393_30486	0	0	TP16
+NM_001017393_30504	0	0	TP16
+NM_001025241_30464	0	0	TP16
+NM_001017393_30504001025241_30513	0	0	TP16

example/boxplot/boxplot.melt.data

@@ -0,0 +1,19 @@
+Gene	Sample	Group	Expr	Rep
+A	zygote_1	zygote	0.8	1
+A	zygote_2	zygote	1.3	2
+A	zygote_3	zygote	1.4	3
+A	zygote_4	zygote	0.9	4
+A	zygote_5	zygote	1.9	5
+A	zygote_6	zygote	1.2	6
+A	2cell_1	2cell	8.0	1
+A	2cell_2	2cell	13.0	2
+A	2cell_3	2cell	14.0	3
+A	2cell_4	2cell	9.0	4
+A	2cell_5	2cell	19.0	5
+A	2cell_6	2cell	12.0	6
+A	4cell_1	4cell	3.2	1
+A	4cell_2	4cell	5.2	2
+A	4cell_3	4cell	5.6	3
+A	4cell_4	4cell	3.6	4
+A	4cell_5	4cell	7.6	5
+A	4cell_6	4cell	4.8	6