plot with 95% ci

[Christos Gkenas]

Hi everyone! I am new to ggplot and I want to ask for some help

I have data from 2 different seasons (wet, dry) from 4 sites of 2 different species and I want to show them in one plot.The plot represents data from shannon diversity index

I have already calculated the mean and the 95% confidence intervals

The overall table looks like this

Season   Sites  Species H (mean)  +95%CI   -95%CI

wet          Ard     PK         0.69           0.84         0.55

dry          Ard      PK         0.39           0.64         0.22

wet         Ard      CL          0.96           1.15         0.72

dry          Ard      CL          0.68           0.93        0.47

wet         Gu       PK          0.64           0.84        0.43

dry          Gu       PK          0.65           0.78       0.52

wet         Gu       CL           1.07           1.22       0.89

dry          Gu       CL           1.17           1.36       0.96

wet         Dg       PK            0.92          1.03        0.82

dry         Dg        PK            0.91          1.09       0.71

wet        Vs         CL            0.96          1.12       0.79

dry         Vs         CL            0.94          1.09       0.75

I would like the plot to show the trend between seasons for every species without a line connecting the error bars.

Thanx for you help in advance

Best

Chris

[Roman Luštrik]

Hi,

the way I see it you have two options:

http://docs.ggplot2.org/current/geom_pointrange.html

or

http://docs.ggplot2.org/current/geom_errorbar.html

See (references to) examples on both links. If you get stuck, feel free to drop another email.

Cheers,

Roman

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[Christos Gkenas]

Hi! thanx for your quick response. i am already doing some progress. However I have 2 questions. I calculated bootstrapped CI and the mean is not exactly in the middle point, how can I deal with this? and is there any command to tweak symbols?

Best

Chris

[Roman Luštrik]

If you have two different CIs (and means) arrange in the same data.frame, where one column specifies from which method the data comes from, you can specify that coulmn in `shape` in `aes()` call. You can add points and their CIs through many geom_linerange (or whichever geom you're using) by specifying the data.frame, a la

geom_pointrange(data = df1, aes(...)) +

geom_pointrange(data = df2, aes(...)) +

Cheers,

Roman

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[Christos Gkenas]

Thank you both for your help! I really appreciate it

I modified a little bit the routine you sent me

(p = ggplot(DF, aes(x = Season, y = H, color = Species, shape = Species)) +

scale_color_manual(values = c("black", "black")) +

scale_shape_manual(values = c(17, 0)) +

geom_pointrange(aes(ymin = LCL, ymax = UCL), size = 1,

position = position_dodge(width = 0.5)) +

theme_bw(base_size = 18) +

theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +

facet_wrap(~ Site, nrow = 1))

and produced the attached plot

I have only one question, do you know how to add caps to error bars?

Best

Chris

Τη Δευτέρα, 5 Οκτωβρίου 2015 - 1:53:38 μ.μ. UTC+1, ο χρήστης Christos Gkenas έγραψε:

[Mary Putt]

Checkout geom_errorbar instead of geom_pointrange.

http://docs.ggplot2.org/current/geom_errorbar.html

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[Dennis Murphy]

Yes, but then one also has to plot the points explicitly with the same
amount of dodging, something like

ggplot(DF, aes(x = Season, y = H, shape = Species)) +
geom_point(size = 3, position = position_dodge(width = 0.5)) +
geom_errorbar(aes(ymin = LCL, ymax = UCL), size = 1,

position = position_dodge(width = 0.5)) +

facet_wrap(~ Site, nrow = 1)

Make the necessary changes to get the appearance you want; for
example, if you want the bars to be less (or more) prominent, use the
width = argument of geom_errorbar(), which is separate from the width
argument of position_dodge().

Dennis