6d99d0a825
Add data to repository
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Add the study data into repository.
2020-11-17 19:49:08 +01:00
27942f784a
secmal: Fix median survival line warning
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Median survival lines are not allowed with "cumhaz" function in
ggsurvplot().
2020-11-17 19:45:18 +01:00
6c4f717793
Merge branch 'secmal'
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* secmal:
Rename plot_survival.R
Add secondary malignancy plots
Introduce initialization function
2020-11-17 18:22:18 +01:00
08f9ddfc23
Rename plot_survival.R
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This scripts is now used to create all plots in this project.
2020-11-17 18:21:54 +01:00
fcd2d330aa
Add secondary malignancy plots
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This adds some plots to show data for the secondary malignacies.
2020-11-17 18:21:54 +01:00
5e7b6007f1
Introduce initialization function
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sma_init() can now be used to load all libraries and the data.
It is safe to call sma_init() multiple times. To forcefully reload the
data call sma_init_force().
2020-11-17 18:17:40 +01:00
a6b5292890
Update README.md
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Add a much more precise description how this repo can be used.
2020-11-17 18:16:57 +01:00
57165dd6d1
Merge branch 'limit-data'
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* limit-data:
utils: Filter all hematologic patients
utils: Filter patient by age
2020-11-17 15:20:21 +01:00
5c26e4100e
Merge branch 'plots-per-dx'
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* plots-per-dx:
survival: Add plots per diagnosis
2020-11-17 15:20:15 +01:00
b81756310b
utils: Filter all hematologic patients
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At this time only solid tumors are important. This is a hard coded
switch, not very useful. But it get the job done and we can decide later
how this can be made better.
2020-11-17 15:12:58 +01:00
c68e536861
utils: Filter patient by age
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The minimum age for this study is 16.0 years or older at time of
transplantation.
2020-11-17 15:05:31 +01:00
95be046985
survival: Add plots per diagnosis
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This adds survival curves per diagnosis. They still look a bit
overloaded.
2020-11-17 14:33:56 +01:00
3c160c37bb
Set global break.time.by value for ggsurvplot
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Substitute manual "break.time.by" values with global which can be used
by all plots.
2020-11-17 14:32:59 +01:00
c087b40f5c
Merge branch 'survminer'
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* survminer:
survival: Improve plots
survival: Change plot function to ggsurvplot
2020-11-17 14:04:07 +01:00
c0c890c78c
survival: Improve plots
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Display a risk table, median survival line and adjust theme.
2020-11-17 13:28:06 +01:00
12ffcd4e38
survival: Change plot function to ggsurvplot
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This will create the plot using the ggsurvplot from "survminer" package.
survminer user ggplot for plotting and comes with some powerful and nice
looking features.
2020-11-17 12:58:51 +01:00
b5634b7f8f
survival: Remove excessive newlines
2020-11-16 22:52:14 +01:00
e1c6279119
Merge branch 'plot-functions'
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* plot-functions:
Add plot_survival.R
survival: Create functions for plots
2020-11-16 22:49:52 +01:00
d6a77d6ebf
Add plot_survival.R
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This helper script can be run from commandline to create the survival
plots.
2020-11-16 22:40:28 +01:00
c3fecc1bf0
survival: Create functions for plots
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Each plot has now its own function. This makes it easier to adjust the
creation and tweaking of a single plot. sma_plot_file() will now call
the individual plot function before saveing the plot.
2020-11-16 22:38:07 +01:00
3dce8a4ea6
Merge branch 'load-function'
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* load-function:
README: List tidyverse as used package
survival: Use new data load function
utils: Add sma_load_data()
2020-11-16 12:40:26 +01:00
d87d3143c2
README: List tidyverse as used package
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Add 'tidyverse' to used package list in README.
2020-11-16 12:37:41 +01:00
27579452c3
survival: Use new data load function
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Load the data with the new introduced function sma_load_data().
2020-11-16 12:27:35 +01:00
f919a31527
utils: Add sma_load_data()
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This function loads the data and adjust some wrong column types. It
shoulb be used from all other scripts to load the data. It the same
source data for all following calculations.
The data is stored inside a 'tibble' from the 'tidyverse' package.
2020-11-16 12:24:20 +01:00
fdd17c0c71
Merge branch 'plot-function'
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* plot-function:
utils: Hide garbage output from dev.off()
survival: Replace manual plotting with sma_plot_file
Introduce plot to file function
2020-11-03 16:57:42 +01:00
815731cbcf
utils: Hide garbage output from dev.off()
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dev.off() prints not usefull messages like "null device 1" when
finishing. This supresses these messages.
2020-11-03 16:55:29 +01:00
439810a544
survival: Replace manual plotting with sma_plot_file
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Replace the manual plotting definitions with the new function to reduce
repitition.
2020-10-22 18:46:30 +02:00
a8c4b327a0
Introduce plot to file function
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sma_plot_file(fname, ftype, title_list, legend_list, fun, ...)
can be used to write plot to a file.
It supports all output filetypes R can handle. Title and legend
arguments can be passed as lists.
All available plotting functions can be used, arguments go into a
variable argument list.
2020-10-22 18:29:13 +02:00
fffd300955
.gitignore: Add csv files
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Ignore all csv files.
2020-10-22 16:41:51 +02:00
42aec82e36
survival: Change scaling to days per year
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The base data was changed from month to years for more precision.
Therefor the scaling of the graphs must be adjusted to days per year
instead of month per year.
2020-10-22 16:38:39 +02:00
e4cead5e99
First version of survival calculation
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This adds a R script which calculates the survival starting at diagnosis
and autologous stem cell therapy.
2020-09-03 17:18:06 +02:00
1c778896f0
Add .gitignore
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Ignore R specific data and generated graphs.
2020-09-03 16:38:29 +02:00
735d67d730
Initial commit
2020-09-03 11:36:11 +02:00
