Preliminary Visualisation of Data
Create preliminary exploratory data visualisations of an entire
dataset to identify problems or unexpected features using 'ggplot2'.
How to install
visdat is available on CRAN
If you would like to use the development version, install from github with:
# install.packages("devtools") devtools::install_github("ropensci/visdat")
What does visdat do?
Initially inspired by
vis_dat helps you visualise a dataframe and “get a look at the data”
by displaying the variable classes in a dataframe as a plot with
vis_dat, and getting a brief look into missing data patterns using
visdat has 6 functions:
vis_dat()visualises a dataframe showing you what the classes of the columns are, and also displaying the missing data.
vis_miss()visualises just the missing data, and allows for missingness to be clustered and columns rearranged.
vis_miss()is similar to
missing.pattern.plotis no longer in the
mipackage (as of 14/02/2016).
vis_compare()visualise differences between two dataframes of the same dimensions
vis_expect()visualise where certain conditions hold true in your data
vis_cor()visualise the correlation of variables in a nice heatmap
vis_guess()visualise the individual class of earch value in your data
You can read more about visdat in the vignette, “using visdat”.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
Let’s see what’s inside the
airquality dataset from base R, which
contains information about daily air quality measurements in New York
from May to September 1973. More information about the dataset can be
The plot above tells us that R reads this dataset as having numeric and
integer values, with some missing data in
classes are represented on the legend, and missing data represented by
grey. The column/variable names are listed on the x axis.
We can explore the missing data further using
Percentages of missing/complete in
vis_miss are accurate to 1 decimal
You can cluster the missingness by setting
cluster = TRUE:
vis_miss(airquality, cluster = TRUE)
Columns can also be arranged by columns with most missingness, by
sort_miss = TRUE:
vis_miss(airquality, sort_miss = TRUE)
vis_miss indicates when there is a very small amount of missing data
at \<0.1% missingness:
test_miss_df <- data.frame(x1 = 1:10000, x2 = rep("A", 10000), x3 = c(rep(1L, 9999), NA)) vis_miss(test_miss_df)
vis_miss will also indicate when there is no missing data at all:
To further explore the missingness structure in a dataset, I recommend
naniar package, which
provides more general tools for graphical and numerical exploration of
Sometimes you want to see what has changed in your data.
displays the differences in two dataframes of the same size. Let’s look
at an example.
Let’s make some changes to the
chickwts, and compare this new dataset:
chickwts_diff <- chickwts chickwts_diff[sample(1:nrow(chickwts), 30),sample(1:ncol(chickwts), 2)] <- NA vis_compare(chickwts_diff, chickwts)
Here the differences are marked in blue.
If you try and compare differences when the dimensions are different, you get an ugly error:
chickwts_diff_2 <- chickwts chickwts_diff_2$new_col <- chickwts_diff_2$weight*2 vis_compare(chickwts, chickwts_diff_2) # Error in vis_compare(chickwts, chickwts_diff_2) : # Dimensions of df1 and df2 are not the same. vis_compare requires dataframes of identical dimensions.
vis_expect visualises certain conditions or values in your data. For
example, If you are not sure whether to expect values greater than 25 in
your data (airquality), you could write: `vis_expect(airquality, ~.x
= 25)`, and you can see if there are times where the values in your data are greater than or equal to 25:
vis_expect(airquality, ~.x >= 25)
This shows the proportion of times that there are values greater than 25, as well as the missings.
To make it easy to plot correlations of your data, use
vis_guess() takes a guess at what each cell is. It’s best illustrated
using some messy data, which we’ll make here:
messy_vector <- c(TRUE, T, "TRUE", "T", "01/01/01", "01/01/2001", NA, NaN, "NA", "Na", "na", "10", 10, "10.1", 10.1, "abc", "$%TG") set.seed(1114) messy_df <- data.frame(var1 = messy_vector, var2 = sample(messy_vector), var3 = sample(messy_vector))
So here we see that there are many different kinds of data in your dataframe. As an analyst this might be a depressing finding. We can see this comparison above.
Thank you to Ivan Hanigan who first
this suggestion after I made a blog post about an initial prototype
ggplot_missing, and Jenny Bryan, whose
tweet got me
vis_dat, and for her code contributions that removed a
lot of errors.
Thank you to Hadley Wickham for suggesting the use of the internals of
readr to make
vis_guess work. Thank you to Miles McBain for his
suggestions on how to improve
vis_guess. This resulted in making it at
least 2-3 times faster. Thanks to Carson Sievert for writing the code
visdat, and for Noam Ross for suggesting
this in the first place. Thank you also to Earo Wang and Stuart Lee for
their help in getting capturing expressions in
Finally thank you to rOpenSci and it’s amazing onboarding process, this process has made visdat a much better package, thanks to the editor Noam Ross (@noamross), and the reviewers Sean Hughes (@seaaan) and Mara Averick (@batpigandme).
Functions in visdat
|miss_guide_label||Label the legend with the percent of missing data|
|vis_cor||Visualise correlations amongst variables in your data as a heatmap|
|vis_guess||Visualise type guess in a data.frame|
|vis_miss||Visualise a data.frame to display missingness.|
|vis_compare||Visually compare two dataframes and see where they are different.|
|typical_data_large||A small toy dataset of imaginary people|
|test_if_dataframe||Test if input is a data.frame|
|typical_data||A small toy dataset of imaginary people|
|vis_expect||Visualise whether a value is in a data frame|
|vis_dat||Visualises a data.frame to tell you what it contains.|
|vis_extract_value_||(Internal) Add values of each row as a column|
|vis_gather_||(Internal) Gather rows into a format appropriate for grid visualisation|
|vis_create_||(Internal) Create a boilerplate for visualisations of the vis_ family|
|compare_print||(Internal) A utility function for vis_compare|
|add_vis_dat_pal||(Internal) Add a specific palette to a visdat plot|
|label_col_missing_pct||(Internal) Create labels for the columns containing the % missing data|
|expect_frame||Create a dataframe to help visualise 'expected' values|
|all_numeric||(Internal) Are they all numeric columns?|
|expect_guide_label||(Internal) Label the legend with the percent of missing data|
|fingerprint||Take the fingerprint of a data.frame - find the class or return NA|
|gather_cor||(Internal) create a tidy dataframe of correlations suitable for plotting|
|guess_type||(Internal) Guess the type of each individual cell in a dataframe|
Vignettes of visdat
Last month downloads
|License||MIT + file LICENSE|
|Packaged||2019-02-15 02:57:38 UTC; ntie0001|
|Date/Publication||2019-02-15 15:30:03 UTC|
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