b3ef8086ec
coxph: Add uni and multivariate analysis
2021-01-17 11:22:06 +01:00
a3c816ad64
coxph: Adjust coxph summary output
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Split HR and CI, print logrank values.
2021-01-17 11:21:05 +01:00
351b26368d
uitils: Remove global data object before reinitializing
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It seems that just overriding the object may not be enough to pure it.
Before loading the data, the variable "secmal" is removed.
2020-12-21 16:39:24 +01:00
9a331a2091
Merge branch 'data-update' into coxph
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Update data.
2020-12-21 11:20:36 +01:00
2db6a44fad
data: Use new dataset
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Update link to new dataset.
2020-12-18 15:38:47 +01:00
79ccaec8fc
data: Update to latest dataset
2020-12-18 15:37:32 +01:00
aa0024256b
data: Reformat data
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Sort data descendig at value uuid
2020-12-18 15:36:30 +01:00
8f07c45f63
coxph: First commit of coxph models
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First univariate with covariates coxph models.
2020-11-25 17:28:13 +01:00
dbfcca9716
Merge branch 'visualize'
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* visualize:
Visualize asct per diagnosis per age
Visualize asct per diagnosis per year
Add basic histograms
Remove unused factor levels from data after limiting
2020-11-19 19:46:44 +01:00
3c517431f6
Merge branch 'fix-library-load'
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* fix-library-load:
utils: Move library() calls to beginning of file
2020-11-19 19:46:39 +01:00
70ed15c2b8
Merge branch 'change-plot'
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* change-plot:
Change default aspect ratio for graphs
Add optional width and height arguments save plots
2020-11-19 19:46:34 +01:00
0be00652e1
Visualize asct per diagnosis per age
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This adds ggplots to visualize the number of ascts per diagnosis per
age in various methods:
* Histogram
* Density plot
* Frequency plot
* Scatter plot
2020-11-19 19:44:33 +01:00
066d6cedf4
Visualize asct per diagnosis per year
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This adds ggplots to visualize the number of ascts per diagnosis per
year in various methods:
* Histogram
* Density plot
* Frequency plot
* Scatter plot
2020-11-19 19:23:29 +01:00
e0faa24f40
Add basic histograms
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This adds some basic histograms to show the distribution of age at
transplatation and year of transplatation.
2020-11-19 19:21:52 +01:00
2175d46379
Change default aspect ratio for graphs
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This adds a 4:3 default aspect ratio.
2020-11-19 16:20:20 +01:00
4762523c20
Add optional width and height arguments save plots
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Sometimes the graphs must have a special size. This adds optional
arguments for width and height.
2020-11-19 16:14:21 +01:00
30c03f01d0
Remove unused factor levels from data after limiting
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After limiting the data there may be factors with empty levels. This can
be confusing and should be avoided.
2020-11-19 13:16:34 +01:00
d96e3c5ed8
utils: Move library() calls to beginning of file
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It seems that calling library() within a function may fail silently.
Moving them out of the function at the beginning of utils.R fixes this.
One particular place, where all necessary libraries are loaded, seem to
be a much easier way than inside a function.
2020-11-18 10:26:45 +01:00
792b42373e
Merge branch 'data'
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* data:
Use data from repository
Add data to repository
2020-11-17 19:50:01 +01:00
2a67cecf0a
Use data from repository
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Starting with this commit, all calculation will base on data/data.csv.
2020-11-17 19:49:22 +01:00
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
