update to visualization

saketkc · Apr 8, 2024 · 3c09102 · 3c09102
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: covmuller
 Type: Package
 Title: A tool to model COVID19 variant prevalence using data from GISAID
-Version: 0.1.2.0007
-Date: 2024-01-21
+Version: 0.1.3.9001
+Date: 2024-04-08
 Author: Saket Choudhary
 Maintainer: Saket Choudhary <[email protected]>
 Description: covmuller can be used to process data from GISAID and 

diff --git a/R/visualization.R b/R/visualization.R
@@ -114,7 +114,7 @@ PlotSequencedPropHeatmap <- function(df) {
 #' @importFrom magrittr %>%
 #' @importFrom tibble deframe
 #' @importFrom ggplot2 aes_string coord_cartesian ggplot geom_bar geom_text labs scale_y_continuous scale_x_discrete xlab ylab guide_axis position_dodge
-#' @importFrom scales comma label_percent label_number cut_short_scale
+#' @importFrom scales append comma label_percent label_number cut_short_scale
 #' @importFrom ggtext element_markdown
 #' @importFrom patchwork wrap_plots
 #' @export
@@ -150,7 +150,7 @@ BarPlot <- function(df, xaxis = "MonthYear",
         size = 3
       )
     } else {
-      df[, paste0(yaxis, "_acc")] <- label_number(accuracy = 1, scale_cut = cut_short_scale())(values)
+      df[, paste0(yaxis, "_acc")] <- label_number(accuracy = 1, scale_cut = append(cut_short_scale(), 1, 1))(values)
       p <- p + geom_text(
         data = df,
         mapping = aes_string(
@@ -180,7 +180,7 @@ BarPlot <- function(df, xaxis = "MonthYear",
       size = 3
     )
   }
-  p <- p + scale_y_continuous(labels = label_number(accuracy = 1, scale_cut = cut_short_scale())) +
+  p <- p + scale_y_continuous(labels = label_number(accuracy = 1, scale_cut = append(cut_short_scale(), 1, 1))) +
     scale_x_discrete(guide = guide_axis(angle = xangle)) +
     xlab("") +
     ylab(ylabel) +

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/Introduction_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/Introduction_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/deps/jquery-3.6.0/jquery-3.6.0.js b/docs/deps/jquery-3.6.0/jquery-3.6.0.js
@@ -8,8 +8,6 @@
  * Copyright OpenJS Foundation and other contributors
  * Released under the MIT license
  * https://jquery.org/license
- *
- * Date: 2021-03-02T17:08Z
  */
 ( function( global, factory ) {
 

diff --git a/docs/deps/jquery-3.6.0/jquery-3.6.0.min.js b/docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
diff --git a/docs/deps/jquery-3.6.0/jquery-3.6.0.min.map b/docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 3.1.12.3
+pandoc: 3.1.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
@@ -13,7 +13,7 @@ articles:
   VariantAnimation-Switzerland: VariantAnimation-Switzerland.html
   VariantAnimation-UK: VariantAnimation-UK.html
   VariantAnimation-USA: VariantAnimation-USA.html
-last_built: 2024-04-04T18:01Z
+last_built: 2024-04-08T11:41Z
 urls:
   reference: http://saket-choudhary.me/covmuller/reference
   article: http://saket-choudhary.me/covmuller/articles

diff --git a/docs/reference/CleanAmericanStates.html b/docs/reference/CleanAmericanStates.html
diff --git a/docs/reference/CleanCanadaStates.html b/docs/reference/CleanCanadaStates.html
diff --git a/docs/reference/CleanIndianStates.html b/docs/reference/CleanIndianStates.html
diff --git a/docs/reference/CleanSouthAfricanStates.html b/docs/reference/CleanSouthAfricanStates.html
diff --git a/docs/reference/CollapseLineageToVOCs.html b/docs/reference/CollapseLineageToVOCs.html
diff --git a/docs/reference/CombineSequencedCases.html b/docs/reference/CombineSequencedCases.html
diff --git a/docs/reference/CountsToPrevalence.html b/docs/reference/CountsToPrevalence.html
diff --git a/docs/reference/CovmullerTheme.html b/docs/reference/CovmullerTheme.html
diff --git a/docs/reference/FilterGISAIDIndia.html b/docs/reference/FilterGISAIDIndia.html
diff --git a/docs/reference/FixDate.html b/docs/reference/FixDate.html
diff --git a/docs/reference/FormatGISAIDMetadata.html b/docs/reference/FormatGISAIDMetadata.html
diff --git a/docs/reference/GeocodeAddress.html b/docs/reference/GeocodeAddress.html
diff --git a/docs/reference/GetFiletype.html b/docs/reference/GetFiletype.html
diff --git a/docs/reference/GetIndiaConfirmedCasesCumulative.html b/docs/reference/GetIndiaConfirmedCasesCumulative.html
diff --git a/docs/reference/GetIndiaConfirmedCasesMonthlyLong.html b/docs/reference/GetIndiaConfirmedCasesMonthlyLong.html
diff --git a/docs/reference/GetIndiaConfirmedCasesWeeklyLong.html b/docs/reference/GetIndiaConfirmedCasesWeeklyLong.html
diff --git a/docs/reference/GetIndiaDailyCasesCumulative.html b/docs/reference/GetIndiaDailyCasesCumulative.html
diff --git a/docs/reference/GetIndiaDailyData.html b/docs/reference/GetIndiaDailyData.html
diff --git a/docs/reference/GetIndiaDeceasedCasesCumulative.html b/docs/reference/GetIndiaDeceasedCasesCumulative.html
diff --git a/docs/reference/GetIndiaHospitalization.html b/docs/reference/GetIndiaHospitalization.html
diff --git a/docs/reference/GetIndianStates.html b/docs/reference/GetIndianStates.html
diff --git a/docs/reference/GetMonthYear.html b/docs/reference/GetMonthYear.html
diff --git a/docs/reference/GetVOCs.html b/docs/reference/GetVOCs.html
diff --git a/docs/reference/PlotSequencedPropHeatmap.html b/docs/reference/PlotSequencedPropHeatmap.html
diff --git a/docs/reference/PlotTotalHeatmap.html b/docs/reference/PlotTotalHeatmap.html
diff --git a/docs/reference/ReadAuspiceInstrument.html b/docs/reference/ReadAuspiceInstrument.html
diff --git a/docs/reference/ReadAuspiceMetadata.html b/docs/reference/ReadAuspiceMetadata.html