Plotting means and error bars (GGPLOT2)

Library (GGPLOT2)

############################################## summaryse############################################### Summarizes data.## Gives count, mean, standard deviation, standard error of the mean, and confidence interval (default 95% ). # # DATA:A Data frame.## measurevar:the name of a column that contains the variable to be summariezed## groupvars : A vector containing names of columns that contain grouping variables## Na.rm:a Boolean that indicates whether to Igno Re NA ' s## conf.interval:the percent range of the confidence interval (default is 95%) Summaryse <-function (data=null  , Measurevar, Groupvars=null, Na.rm=false, conf.interval=.95,. drop=true) {library (PLYR) # New        Version of length which can handle NA ' S:if na.rm==t, don ' T count them length2 <-function (x, na.rm=false) { if (na.rm) sum (!is.na (x)) Else length (x)} # This does the summary.    For each group's data frame, return a vector with # N, mean, and SDDatac <-ddply (data, Groupvars,. Drop=.drop,. Fun = function (xx, col) {C (N = Length2 (Xx[[col]], na.rm=n      A.RM), mean = mean (Xx[[col], na.rm=na.rm), SD = SD (Xx[[col]], na.rm=na.rm)}, Measurevar) # Rename The "mean" column Datac <-Rename (Datac, C ("mean" = Measurevar)) Datac$se &lt     ;-Datac$sd/sqrt (datac$n) # Calculate standard error in the mean # Confidence interval multiplier for standard error # Calculate T-statistic for confidence interval: # e.g., if conf.interval are.. 975 (Above/below), and use Df=n-1 Cimult <-qt (CONF.INTERVAL/2 +. 5, datac$n-1) datac$ci <-datac$se * cimult return (DATAC)}########## #################################### Sample data############################################ #library (ggplot2) TG <-Toothgrowthhead (TG) TGC <-Summaryse (TG, measurevar= "Len", Groupvars=c ("supp", "dose")) tgc################## ############################ Line graphs############################################## standard error of the Meanggplot (TGC, AES (X=dose, Y=len, Colour=supp)) + Geom_errorbar (Aes (Ymin=len-se, Ymax=len+se), width=.1) + geom_line () + Geom_point () # The ErrorBars overlapped, so u Se position_dodge to move them horizontallypd <-Position_dodge (0.1) # move them.-The left and Rightggplot (TGC, a Es (X=dose, Y=len, Colour=supp) + Geom_errorbar (Aes (Ymin=len-se, Ymax=len+se), width=.1, POSITION=PD) + Geom_line (p OSITION=PD) + geom_point (POSITION=PD) # Use 95% confidence interval instead of Semggplot (TGC, AES (X=dose, Y=len, colour= Supp) + Geom_errorbar (Aes (YMIN=LEN-CI, Ymax=len+ci), width=.1, POSITION=PD) + geom_line (POSITION=PD) + Geom_poi NT (POSITION=PD) # Black error Bars-notice the mapping of ' Group=supp '--without it, the error# bars won ' t be DODGED!GGPL OT (TGC, AES (X=dose, Y=len, Colour=supp, Group=supp)) + Geom_errorbar (Aes (YMIN=LEN-CI, YMAX=LEN+CI), colour= "Black", WI  Dth=.1, POSITION=PD) +  Geom_line (POSITION=PD) + geom_point (POSITION=PD, size=3) # A finished graph with error bars representing Error of the mean might # look like this. The points is drawn last so then the white fill goes on top of# the lines and error Bars.ggplot (TGC, AES (X=dose, Y=len, C Olour=supp, Group=supp) + Geom_errorbar (Aes (Ymin=len-se, Ymax=len+se), colour= "Black", width=.1, POSITION=PD) + ge Om_line (POSITION=PD) + geom_point (POSITION=PD, size=3, shape=21, fill= "white") + # are filled circle Xlab ("Dose (M                     g) + Ylab ("tooth length") + Scale_colour_hue (name= "Supplement type", # Legend label, use darker colors  Breaks=c ("OJ", "VC"), Labels=c ("Orange Juice", "ascorbic Acid"), l=40) + # Use darker colors, lightness=40 ggtitle ("The Effect of Vitamin C on\ntooth growth in Guinea Pig S ") + expand_limits (y=0) + # expand Y range scale_y_continuous (breaks=0:20*4) + # Set tick every 4 THEME_BW () + Theme (Legend.justification=c (1,0), Legend.position=c (1,0)) # Position legend in bottom right############################################## Bar graphs#####################  ######################## # Use dose as a factor rather than NUMERICTGC2 <-tgctgc2$dose <-Factor (tgc2$dose) # Error Bars represent standard error of the Meanggplot (TGC2, AES (X=dose, Y=len, Fill=supp)) + Geom_bar (position=position_dod GE (), stat= "identity") + Geom_errorbar (Aes (Ymin=len-se, Ymax=len+se), width=.2, # W Idth of the error bars Position=position_dodge (. 9)) # Use 95% confidence intervals instead of Semggplot (TG C2, AES (X=dose, Y=len, Fill=supp)) + Geom_bar (Position=position_dodge (), stat= "identity") + Geom_errorbar (Aes (ymin= Len-ci, Ymax=len+ci), width=.2, # Width of the error bars Position=po Sition_dodge (. 9)) # #A finished graph might look like This.ggplot (TGC2, AES (X=dose, Y=len, Fill=supp)) + Geom_bar (Position=position_dodge () , stat= "Identity", colour= "Black", # Use black outlines, size=.3) + # thinner lines Geom_e                  Rrorbar (Aes (Ymin=len-se, Ymax=len+se), size=.3, # thinner lines width=.2, Position=position_dodge (. 9)) + Xlab ("Dose (mg)") + Ylab ("tooth length") + Scale_fill_hue (name= "Supplement t  Ype ", # Legend label, use darker colors breaks=c (" OJ "," VC "), Labels=c (" Orange Juice ", "Ascorbic acid") + Ggtitle ("The Effect of Vitamin C on\ntooth growth in Guinea Pigs") + scale_y_continuous (breaks= 0:20*4) + THEME_BW ()

REF:

http://www.cookbook-r.com/Graphs/Plotting_means_and_error_bars_%28ggplot2%29/

Http://www.rdocumentation.org/packages/bear/functions/summarySE

http://www.cookbook-r.com/Manipulating_data/Summarizing_data/

Http://www.inside-r.org/packages/cran/rmisc/docs/summarySE

Plotting means and error bars (GGPLOT2)